Submarines. I've been under the impression that you're supposed to require Sonar to detect, and torpedoes to fire at them when submerged; this would make them ideal for defense, area control and (in the case of fabber subs) sneaky building. But as far as I can tell, they get shot at as readily as anything else, making them strictly inferior. Is their diving mechanic just not implemented? Meanwhile, Commanders can walk along the sea floor and survive easily as shots rain down from above - including shallow torpedoes. I suspect that the latter part of that, at least, is a bug.
Yes, naval is still being worked on. Subs haven't gotten much love yet but hopefully that will change soon.
Subs will actually work as you have said, T2 ones will even build nukes. Commanders are currently invulnerable in water unless you asterid smash them or nuke them.
Underwater Commanders can be hit by projectiles, as projectiles do pass through water. Though it's exceedingly difficult to order an attack ground command close enough. Ah, the joys of a half-baked navy.
