1. For the most part, after the last book the Animorph's parents weren't talked about much. As far as we know, Jake's parents become controllers but we don't learn whether or not they were freed at the end. Marco's mother was freed and his father went to live with them at the Hork-Bajir camp, best guess is that they lived through the war. Cassie's parents went to live with them at the Hork-Bajir camp as well, and probably lived after the war. Rachel's mother went to live with them at the Hork-Bajir camp, we know she survived the war, but I don't remember anything being said about her mother. Tobias' mother went to live at the Hork-Bajir camp, but she never remembered him, best guess is she lived too.
2. Probably the best explanation was that the buffa-human book was written by a ghost writer and the David books weren't. =/
3. I believe it was book #31. There are a lot of things in the book that people weren't a real fan of, including how weirdly the situation with Tom/the Yeerks was handled.