^ If Federation starships were capable of operating under water, why would they NEED submarines?
Agreed. In TAS, if you accept it as canon, we saw special shuttles capable of landing on water. If you need a special shuttle for that, then it's likely that a conventional shuttle cannot. Probably the same for a starship.
In TNG's "Brothers," Picard is lured by some odd underwater project. Why is that a special undertaking performed by a different organization, if Starfleet can't just go underwater with a starship and -- presto! -- instant sea colony?
Not canon, but one of the Shatnerverse novels stated that ships can go under just fine. The problem is coming back out to space, when the water turns to ice and cracks the vents, etc.
Finally, if you can adjust screens to go underwater, why do we distinctly see weathering on the TOS Enterprise? It appears that at least navigational deflectors leak a bit, to create the gray streaks on the hulls and pylons. I've never thought of shields cranked up to max as impenetrable bubbles, possible of screening out all dust, all water, and so on.
And what's the fun of such super-shields, anyway? It reminds me of Superman in 1940s radio drama. The writers were stuck with such an invulnerable character that they had no suspense. That's why Kryptonite was invented.
Anyway, we'll all know the truth when the next nu-Trek opens.