Like Athenian I always considered the Tower of the Gods as a water temple. I mean, I know the game doesn't have a specific "Water Temple", but it also doesn't have a specific "Fire Temple" or "Forest Temple". There are just temple's themed like that. Dragon Roost Cavern has fire, Forbidden Forest has... forests, and the Tower of the Gods has water. So really, to me it's just like a water temple.
I would assume however, that one of the two temples that Iwata said were cut from the game was a water temple where you got Nayru's Pearl. Who knows, maybe it was inside Jabun, and you went in there with the King of Red Lions. Or maybe not. I think that I can make the assumption that the addition of water to the Tower of the Gods may have been an afterthought because of the removal of the water temple. Maybe they just took some of the water puzzles from the old water temple and put them in the beginning of the Tower of the Gods? Who can say.
Either way, a Zelda game doesn't NEED a Water Temple. Phantom Hourglass didn't have one. And I found that the different themes in Wind Waker were a nice break from the usual.