The underwater missions are relatively easy so this won't matter all that much. In early game, ADS (against deep ones and gilldogs) or Gas Cannon with AP clips. Landmines in the early game. You get some sonic later (I used blasta rifle in my previous game), but I suppose you might be able to skip sonic completely as well. Once you progress in the underwater arch, and missions with more cover, melee weapons (for example katanas, battle axes, tritanium knives, stun rods if you need a capture) have been my primary weapons. Underwater missions are also a good use for training PSK (dagon's staff) on closer range.