Ten possible entrances to Pharloom Bay listed from least to most likely, since I have nothing else to do with my time rn
For reference, existing Pharloom Bay related map assets and ACMI exhibition screenshots:
Based on these, cut dialogue from Zylotol, and the Pharloom Bay related assets in Weavenest Murglin (including a lore tablet that appears to directly reference the place) we know that Pharloom Bay would almost certainly have connected to Bilewater, so with one exception all of the possible entrances listed here will be in Bilewater. I think it's worth noting that it's somewhat rare for an area to only have one connection to other area(s) in Silksong; Weavenest Atla, Mount Fay, and Verdania each have one connection, the Cradle has one connection via Cogwork Core that then turns into a Choral Chambers connection in Act 3, and the Abyss has one connection via Deep Docks plus a one-way connection in the form of the Abyss climb, but all of the other areas have at least two connections to another area, albeit often with only one initially accessible entrance (like Hunter's March or Sands of Karak). Based on this and what looks like a passageway extending up to the top right in the April 2021 version of Pharloom Bay, I wouldn't be surprised if there were at least two connections to Bilewater or even to other areas of Pharloom proper (not counting areas in the Sea of Sorrow itself), with only one of them being initially accessible from Bilewater and the other one(s) being unlocked from the Pharloom Bay side.
The only possibility that isn't in Bilewater, which is one of the main reasons it's least likely IMO. The others are that there's nowhere obvious to put a breakable wall, it seems to be too high up to fit with the probable layout of Pharloom Bay, and the Pale Lake in general has plenty going on already (a Craftmetal, Fleatopia, and both the Flea Festival and Mister Mushroom quest in Act 3).
-#9: Shakra's master's room
This room has the same problems of being too high up as the Pale Lake and having no obvious breakable wall points, and as the conclusion of Shakra's questline, it probably has too much emotional/narrative significance to just be an entrance to another area. This also introduces the problem of the map for Pharloom Bay, since this room only becomes accessible once you've bought all of Shakra's maps. Most of the area maps are bought from Shakra, with four main exceptions: Citadel-affiliated areas, like the Citadel itself, the Underworks, the Slab, and Putrified Ducts (kinda), since Shakra refuses to go there outside of helping in the Forum; Weavenest Atla, which she couldn't get into due to lacking a Needolin; the Abyss, which she couldn't get into due to lacking the key for the diving bell; and Verdania, which she couldn't get into due to it only opening up in Act 3, by which point she was occupied as Bellhart's protector. If Pharloom Bay is intended to be part of a normal playthrough's progression, there's no reason to think she wouldn't sell its map, so while it is possible that the Pharloom Bay map is obtained some other way, it seems likely that it'll end up being a prerequisite for Trail's End like the other maps, which makes the room unlocked in Trail's End implausible as an entrance. I do think there might be something new with Shakra's master at some point though, even if it's not in Sea of Sorrow; maybe she gets a fight in Silksong's version of the pantheons?
Despite the use of Pharloom Bay assets here and (currently) nowhere else in the game, I don't think Weavenest Murglin will have an entrance. It seems to be too low down, and furthermore, no other Weavenest aside from Atla has a connection to another area, with Atla being unique in that it's its own area entirely. The gameplay purpose of the Weavenests seems to be as holding zones for tools (like Silkspeed Anklets in Cindril, Weavelight in Atla, or the broken Silkshot in Murglin), abilities (like Sharpdart in Karn or Silk Soar in Absolom), other upgrades (like Farsight in Absolom or Eva's upgrades in Atla), and/or lore (like Eva in Atla or the map in Cindril); if Pharloom Bay were accessible through a Weavenest it would become one of only three Acts 1-2 areas to be gated by the Needolin, the others being Weavenest Atla and the Citadel proper (which have clear lore reasons for Needolin gating), and Murglin would become the only Weavenest with multiple entrances and a purpose beyond upgrades and lore. I don't think this is all that likely. Instead, I think Murglin uses Pharloom Bay assets because it's an "off-theme room" that resembles a neighboring area without actually connecting to it; we see these in both games with the Marrow room in Weavenest Atla, the Sands of Karak coral at the bottom of the Slab, and the Ancient Basin-themed Sharp Shadow room in Deepnest, for example.
-#7: The room with the hidden bench
This is fairly close to where I think that tunnel in the top right of Pharloom Bay might lead, but the wooden wall here means the probability of a breakable wall is lower than usual, and it'd be kind of weird to use the same hidden room to gate an entire area as well as a bench.
-#6: The vertical room in lower Bilewater
This room probably has the same "too low" problem as Murglin, though it's high enough that it's still a possibility and it doesn't have the same one-entrance layout that constricts Weavenests. Since this is in the part of Bilewater accessible without Faydown Cloak, it seems entirely too early in the area for a connection, since Silksong area design usually puts connections to other areas towards the end of the current area (see the entrances to Bilewater and the Mist from Sinner's Road, or the entrances to Putrified Ducts from Bilewater and Memorium). It also doesn't really have much going for it, which is kind of a theme with this batch of possible entrances.
-#5: The vertical room with the Swamp Squits leading to the Slubberlug room
This room is close to the right elevation, but it's so close to the Slubberlug room that the latter kinda crowds out any connections to Pharloom Bay, and if they're going to put the entrance close to the memorable Slubberlug room they would probably just put it in the Slubberlug room. Plus, while it is gated by Faydown Cloak, it's still fairly early in upper Bilewater, and I doubt Team Cherry would want to let us cut our Bilewater suffering exploration short by giving us an early out into another area.
This room is basically just the previous one but better in every way; it's at a good elevation for the upper right tunnel, it's gated by suffering in the form of the Slubberlugs (fuck the Slubberlugs), it isn't crowded out by any other rooms, and there are even what looks like fishing nets in the foreground, perfect for a room connected to a coastal area. However, there isn't an obvious spot for a breakable wall, and the Slubberlug room already serves to house a Mask Shard, with the other challenge rooms that do that tending to be entirely focused around said Mask Shard (like the Garpede platforming room in Deepnest or Skull Cave in Far Fields). Reasonably possible, but not my top choice.
This one has pretty much all of the same characteristics as Shakra's room (discussed below), except for the lack of an obvious gate and being slightly lower down than Shakra's room. If it weren't for the Mask Shard I'd place this below the Slubberlug room because of the latter's nets, but while the Mask Shard does knock it down below this one, that's not because the Wardenfly room is significantly better. Not much else to say here.
I think this room is very likely to be an entrance... if anything, too likely. It's small enough that a tunnel to give Pharloom Bay some more space from Bilewater could easily fit, it's at the edge of the gap in lower right Bilewater where Pharloom Bay seems to have once fit, it has a collapsed gate or door of some kind at the end that could easily be broken or removed to lead into Pharloom Bay, and it doesn't do much once you've bought Shakra's map except host a one-time Covetous Pilgrim spawn. However, this is way too early in upper Bilewater for us to fully experience the suffering exploration of the area, and these are the same people who put an obvious closed gate between Fungal Wastes and City of Tears with no way to open it, so while I do think that this will be an entrance unlocked from the Pharloom Bay side, constituting a shortcut from the Bilewater bellway to the barnacle village, I don't think it's where we'll originally enter the area. Instead, I think we'll enter through...
-#1: The shell shard room to the right of the platforming room en route to Groal
Hear me out. If that second connection in the upper right passageway exists, I think this is where it's going to connect. That wall with a wooden brace is absolutely ripe to become a breakable wall, since a brace often indicates a breakable wall in both games; it's so far into the Groal runback that it ensures you've suffered through explored most of upper Bilewater; and an initial entrance in the upper part of Pharloom Bay would force the player to explore the entire area to get to the barnacle village and the submarine, with the shortcut back to Shakra's room unlocked towards the end in keeping with Silksong's area design philosophy. This lets it feel like a natural part of the game world; if you can just beeline straight to the village and the submarine from Shakra's room, Pharloom Bay becomes a pit stop en route to the Sea of Sorrow with some optional exploration tacked on top, but if you're forced to explore the whole area to get to the next one like every other area in the game, it not only makes the expansion feel more natural to the base game but pads out the new content that people will see, which is better for both new playthroughs and ones completed in anticipation of the DLC. I originally started this post thinking that Shakra's room would be the top contender, but the more I've thought about it the more I've become convinced that it's a red herring unlocked from the other side, and that Silksong's area design principles indicate that this will be where we first enter Pharloom Bay. The one issue is that it might be a bit too high to make this work if the 2021 maps are accurate to the version that'll be in Sea of Sorrow, but it'll have been five years since that version was accurate, maybe Team Cherry added more rooms in upper Pharloom Bay to account for this.
