Yeah, it is a bit strange that they stop filling when one has enabled “fill empty houses”. I have that option on in some of my saves as well, and in one save where my sim lives in Henford-on-Bagley it has only been empty houses in Willow Creek and Oasis Springs that have been filled despite my having played through several sim years (I do have aging off, though). In another save where my sims live in San Myshuno two empty apartments were filled, but other than that it was once again only empty houses in Willow Creek and Oasis Springs that had randomly generated townies move in. No one was moved in in any of the other worlds, which is pretty odd.
As for your 100 baby challenge, do the dads have to have a house? Or has the game simply stopped generating random townies altogether?