Ooh, ooh, new info on patch page!

[Poopsi]

Thematically I never envisioned R'lyeh as leaving totally empty wastelands behind, but rather that you would see a diminished population grieving over their relatives who went mad and marched of to follow the dream. I wouldn't really like to see R'lyeh having tons of 0-population provinces.

I dont see it as really killing everyone. I see the population loss as signifying that those provinces no longer have regular humans, because they have either been murdered by void cults or void beings, joined void cults, or mutated into horrible creatures. In any of those scenarios they are basically irretrievable as population, and are simply part of the dreamlands. (My own thematic take)