Yeah but you have to remember how Kisame sensed it. The reason that shadow clones in particular are hyped up is because they make it hard to find the real one. An example would be how Neji couldn't find the real Naruto easy by looking at the chakra comparison between the clones. Kisame does the same thing in a way, he senses using chakra itself, so he should logically be confused as well or so I'd figure.
Wouldn't Sasuke be drowning if he's in the water with Naruto? Unless he can make an air bubble big enough for him + Susano'o somehow xD