Hans Uberman

Remember we're talking about the game, and how it does things, not necessarily real life physics, or how it should be.

In-game during a storm, you go slower while producing the same amount of energy (e.g. - one third power), but underwater you go the same speed as always. I think the game simply considers underwater to be far more calm, and doesn't alter the speed in any way. As far as the game is concerned, on the surface, rough waters slow you down, underwater there is no effect simulated from currents, waves, or other phenomenon.

Also, while waves are generally moving up and down, they do indeed forward to a degree. Boats not only go partially through waves, but expend energy traveling up them.