Your first point isn't very good. . . Ganondorf is referring to Tetra's dreams, so what he's saying probably does not apply to the real ocean. And there is obviously wild life in the water. Flying fish thingies, sharklike monsters, map fish, squids of all sizes, sea gulls (suggesting that there are normal fish that they must eat), and the mere fact that Outset is a fishing village. Your second point, however, is totally reasonable, and I agree to a certain extent.
I'm not actually sure if the castle was brought back after Ganondorf was destroyed; that could be. Otherwise, however, you'd probably be right.