This is a simple matter of harmonious methods of coexistence having been neglected. The vast majority of maid packs (or "staffs") are not in fact wild, but feral, and are comparatively easy to re-domesticate if you know what you're doing. Why else do you think they're called "domestic servants"?
But maids require enrichment. You don't have to worry about space — a staff will generally only move into an area that's already large enough for its needs — but they still want to feel useful. They need ingredients for meals and materials for clothing, but if these are provided and it is clearly communicated which stores contain the supplies they need, they will be absolutely meticulous about sticking to them. Managing such matters is easier if you can promote one of your maids to Cook or Butler: these senior positions in a staff server vital regulatory functions in keeping the rest of the staff from either becoming bored (which can cause them to get inventive in undesired ways) or overtired (which can cause internal conflict). A settled staff will either promote its own senior members, or ask you to make the selection. If you can achieve both, so much the better: a well-matched Cook and Butler pair can be among the most potent organising forces on forty-five planes of existence. Note that, in smaller staffs, a Housekeeper may arise instead of a Cook, but is perfectly capable of performing most of the same jobs. Lack of Senior Staff is the number one cause of maid friction. If items are being misfiled or moved from day to day, this is a result of not allowing your staff to spawn seniors.
Learning to live with a staff certainly comes with a period of adjustment may make your dungeon livable, yes, but they were bred to serve the aristocracy and as such have an innate understanding that some living areas are meant to be fancier than others — so show them that some areas are for residents, some for staff, some for guests, and some for prisoners and they will maintain each accordingly. Maids are also capable of being effective dungeon guards, being naturals at observation and stealth. They won't be overpowering prisoners or intruders, but they are perfectly able to trap them and you may even find your staff developing rare "battle-maid" variants.
Your reagent cupboards will be cleared out, yes, but if you put a sheet out nearby with a heading such as "reagent inventory" then you will find that rather than thrown out they will instead be organised, and you'll get a list detailing exactly how much of which reagents you have in stock, too. You're worried about your dragon dung being tossed? Have a quick word with a maid and ask for a container to keep it in. Don't expect to be presented with such a thing — rather, within a day or two you'll walk into your workshop and find that a dragon dung bin has quietly been installed, labelled, and filled.
Valuables going missing is a concern. Labour must be rewarded and maids know this as well as any human. The trick here is to either leave a labelled pay packet out regularly or, if you've managed to obtain a Butler or Housekeeper, speak to them directly and explain how to draw from your designated treasury. (Look, you're of a social stratum to be maintaining a mansion, castle, or arcane tower. You have a treasury, even if you don't realise it yet. You may have to ask your Butler to oversee its organisation in the first place, though.)
In short: once a pack of feral maids moves into your property, yes, they are difficult to get rid of — but treat them well and you'll never want to.
