I haven't been to the theives guild hideout in quit a while and the floor where the pool of water is deeper, and also brighter (the whole rooms alot brighter actually), i know its deeper because i use to jump over the fence and now i cant.
the room im talking about is the one with the fence/other merchants
That room with all the vendors that you're referring to is the Ragged Flagon in the TG. The other wide open room is the one you can sleep/store your stuff/eat/live in is the Cistern.
I haven't seen any patch (or mod) to date that changes any of this. Especially since these areas involve a major faction quest line. What version are you running?