That sort of uniform genetic preference in a people takes a good couple of thousand years (about 100 generations or so) at the bare minimum. Albinism is more likely to an extent, since less pigment would form reactively on account of the lack of sunlight, so very pale skin would be common, but pigment (and the ability to produce it) would still exist within the body. I'd expect any obvious mutations to be a result of an external influence, perhaps a bacteria which grows in the air recycling system, or a synthetic nutritional supplement in the food algae which had unforeseen consequences.
Of course, you could go full-on crazy and have some sort of gene therapy designed to assist with deep-sea living. That's a whole can of worms waiting to be popped open right there, but again, probably not appropriate for the period in which these habitats were formed/settled. The eldritch angle offers options for this I suppose, but it all depends on how much 'Eldritch Tech' you really wanna introduce.