[TorpX]

In real-life, I think most submarines cut through the waves, instead of riding over them. I believe this is due to their low reserve buoyancy (meaning they are almost heavy enough to sink). However, props did come out of the water at times, and reduce speed. The S-class were known to have poor sea-keeping characteristics, for example.

Don't expect too much from the game. I've noticed the same thing about the waves; the water will push up under the sub, and cause it teeter atop the wave, until it slides off. There have been attempts made to make the waves/effects more realistic, but there are limits to what can be done.