Yes, townies retain their family trees if they have any. Moving them in via normal channels may cause memory loss, though.
Is there a way to move them in via non-normal channels to prevent memory loss? Or is it just something to be dealt with? I've noticed that the townies I have moved in with families tend to keep their relationships with people they've met, but don't recall any of the memory-inducing things they might have done with those people.