London in the "Dark Ages" didn't have aqueducts. But Londinium was part of the periphery of the empire, and it also never had aqueducts. There's not that much information to be gained by cherry picking the elements of the central core of the Roman Empire and asking why they weren't present in far flung areas in the post-Roman era.
Skeletons show that people were relatively healthier (at least in the periphery) after Rome had fallen than when Rome had dominated these regions.