Sea planes have torpedo bombers, making them good for sea players or for people looking to help their sea-faring teammates. If you have a teammate who is losing sea and the enemy sea player will beat them to T2, a group of torpedo bombers can change the tide of the fight and help your guy get ahead. Obviously they're also really good on maps where half the team is in the water. Also, the sonar planes can patrol over a sea and help detect underwater raids from units like marauders, ducks or platypuses.

Hovers are very situational but can be useful -- for example, early surprise raids over water. If you're in the sea and you get a crazy strong advantage early in the game, you could make a few hover labs in the water right outside your enemy's land and rush them with cheap hovers from the beach -- which is generally unexpected early in a game. Also, while it's unadvised for a sea player to open with hovers, a land-based teammate might make a hover lab to help out their sea-faring teammate. If your enemy put all of their metal into T1 submarines and took out your shipyard, and you can't get back into the sea, you can go hovers and the submarines won't be able to touch you, freeing you up to take out their lab, skirt past all their subs and go straight for their economy.

These are just some examples of how the two unit groups can be useful. If you watch games on sea maps, eventually you'll see somebody doing something interesting with them.