I could see this leading to two development paths (at the same time, not either or);
Multirole Submarines:
Basically the a submersible Naval version of Multirole Fighters, that is equipped with some Torpedoes, Missiles and Guns, but not alot of each, designed to basically play a variety of roles against weak targets or as part of a Screening fleet.
Amphibious Warships:
Essentially Warships that are fully submersible (but not to depth) or partially submersible (the larger ones), in the first kinds case this would allow smaller warships to travel just under the water, making them all but invisible to anything but Radar or in clear waters, while in the latter's case this would allow them to appear smaller than they are, thus confusing the enemy/making them let their guard down, they may as well have the part that stays above surface designed to look like a class of smaller ship in use to further this affect.