Yes, you do have the ability (with the Bathymetry option) to go deep and explore the ocean floor with either the Submarine (Ohio Class) or the Neptune Submersible.Looking at the description of the Academic version it states that it spans from deep underwater to space.
So where are the submarines?
Disclaimer--I don't own Prepar3d yet.
It's like Daube said, it's not like there's amazing things to explore and find on the bottom. Mostly I think there are a few missions that place you in a specific area so you can locate a sunken ship I believe, but to just take it into a Lake or into the Ocean somewhere. . .you won't see much.Wow, I hadn't seen that sneak in there! I'm surprised LM didn't make more of a song-and-dance about it!