this is kind of a stupid topic, but because i am equally as stupid i will engage with it nonetheless.
brown doesn't necessarily mean black. there are so many people across this planet that are brown without being black.
also, sue is designed by a japanese man who is influenced by japanese character designs. japanese character designs (like most character designs that abstract reality) usually just exaggerate real features. anime tends to represent tanned characters as straight up brown. its weird, but par for the course within anime.
she's brown (maybe just tanned) with green hair. the other humans also have green hair. and if i recall, itoh was also brown wasn't he? and the sakamotos were kinda tan as well. maybe theyre just darker-skinned asians or just tanned. maybe the humans of cave story have different races than we do.
i don't think too hard when it comes to cave story design choices like this. pixel probably just said, "brown and green go well together. they're very natural colors. i will design sue's human form with this in mind" idk.