About all the Zelda games have always had temples with a focus on forest, fire, and water, not necessarily in that order nor even all that obvious in their use of the element, but the elements have always been there. Will there be a clear and defined "water temple"? Maybe not, maybe just a temple that utilizes water elements without actually requiring swimming or the like, but even with SS's focus on innovation for the series I doubt they're gonna remove the basics, maybe just disguise them and spruce them up.
With the possibility of diving and breathing underwater, I can only hope that they will bring that back. WW was the only one of the big 3D titles that didn't feature diving, and that was mostly because it would have been too much hassle giving Link diving abilities in a giant ocean (hard to define a limit to the dives). Swimming around underwater is definitely something I enjoy greatly, though I'm not sure the likelihood of it happening since there's a bigger focus on the Sky this time around, but that still doesn't rule out the possibility.
The information we have on SS is rather scarce. We only have a basic idea of the plot, and the demo showed a location that won't even be featured in the actual game according to interviews. We really have no idea then what the overworld is gonna be like, what species we are going to encounter. Will we see the Zoras? There's nothing that really points in either direction. If the Zoras are present, then I really think we WILL see an underwater system, as most all the games with Zora in them also have the Zoras providing Link with some swimming/diving ability. If the Zora's are absent, we can still have a diving system, but Nintendo will have to be more creative with how they give that to us, and knowing Nintendo, I'm sure they'll find a way if they want. Maybe I'm just being optimistically hopeful, since I love swimming underwater and I love water dungeons, but at the same time it's certainly very possible that water elements like that will return. Who knows, we may even get more (I'm personally hoping for an underwater city X3).