Demy-cat

I think Mint Choco is my best example when thinking about this concept. Outside of his dough color, nothing about his character codes him as black as far as I'm aware. He's just a musician. The icing representing his hair is an unnatural color with a texture that best translates to straight hair, and his eyes are blue. The only thing coding him as black or as a poc is his dough color.

Often in anime you see characters like this that I call "mythical POC". they have no distinctive facial features that point to any racial group, no hair texture, and the color of their eyes and hair is some unnatural color or a color way lighter than any person of color would usually have naturally. The only feature denoting them as a person of color is their skin being clearly brown. Despite this, they cannot ever be white because white people do not have dark skin, making them fictional portrayals of people of color. Lightening their skin is still an intentional and racist action.

Since the characters in cookie run aren't humans and don't have skin, the waters get a little muddy, but In my opinion? The previous logic still applies. Despite whatever racial coding is or isn't present, these humanoid characters are still being represented with a range of different "skin" tones. You could argue for a different story if every cookie had the same base gingerbread dough, but they made a choice to include diversity in "skin" tone and they made a choice to make the cookies extremely humanlike so much so that a lot of them could be considered chibi human designs moreso than cookie designs.

If they really wanted Dark Cacao Cookie and his kingdom to all be representations of light skinned purely Korean people, making them based on the flavors they're based on and making them all have dark dough was an idiotic choice. If the human design came first and the cookie designs came later, the cookie designs would be "blackwashing" at best and straight up blackface at worst considering how humanlike the cookies are. There are light cookies based on Korean culture like Okchun cookie that in my opinion have nothing wrong with them. They could've been based on any other flavors and looked any other way.

Even if it isn't exactly realistic for a kingdom inspired by Joseon-era Korea to be comprised exclusively of dark skinned people, that doesn't matter because 1. It's only inspired, not some. Faithful realistic fiction and 2. It's fiction!!! It's fantasy!!!!! None of this is real!!!!!!! It's not realistic for Golden Cheese cookie to have orange/gold eyes or for Hollyberry Cookie to have pink eyes, and yet their human designs have them! They don't represent any one racial group with full accuracy because they're fictional, "mystical" characters! That does not mean it's okay to specifically intentionally whitewash them when their original designs are darker!

(Speaking of those two, they're also lighter than their cookie designs. Even pv and white lily get the lightening cream treatment. Dissapointing but unsurprising but that's a trend with this company to discuss another day)

Tldr: Dark Cacao isn't black coded and a lot of "darkskinned" cookies arent black coded either, but that doesn't mean it's okay to represent them lighter because they were intentionally designed as characters with dark "skin" from the start.