I can only answer part of your question. The Tower set I just bought does have a water mark on it. Unfortunately, I can't tell you how to identify it from the box. The CS&C set I got did not have a water mark, but it wasn't really necessary. The four siege tiles are unique and the shrine tiles from the big box have a water mark, so you can differentiate them from the ones in the mini-expansion that don't. That's how I tell them apart.
The Catapult is worthwhile if only for a few unique tiles. I don't mind playing with it at all, it can be fun. There is a fan-made expansion here that uses the tiles without the catapult itself. It's called The Jester and the Minstrel and it is available in the public downloads
HERE (along with a bunch of other great expansions). It adds only two neutral meeples and looks like fun.
I hope that helps a little bit.
