On the point about ballistae being able to knock down walls and towers, yes it does seem rather silly. There was some discussion about this in one of the modding threads, the end result being that someone figured out not only how to make the ballista not damage walls/towers/etc, but consequently also not even attempt to target them IIRC. If anyone wants the "fix" I imagine it would be pretty easy to locate in the modding area.

This may come with pitfalls, though. I have no idea if the AI still considers the ballista an assault-enabling unit if it can no longer damage fortifications (of if it indeed ever considered it assault-enabling). If it does, then it's possible the AI could start a siege with absolutely no way to breach the walls or gate at all. I haven't seen the AI assault using only a ballista that I can remember, but that doesn't necessarily mean it doesn't try it...