It is also possible that the fact that the Enterprise is under the water, may be called back when another starship falls into the ocean, to foreshadow the fact it is not lost.
Good Grief, that's thing that annoyed me the most. It's like Abrams can't stand the fact that the Enterprise is you know a frakking STARSHIP and needs to be in space. No, that's been done to death so we need put her in the middle of the desert or underwater. In the next movie Abrams will be making it swim through jello because its Kewl. Bah!