I noticed this too. It looks like the boat is levitating at a fixed height and the waves go over, around and thru the boat instead of crashing against it. When I watch it seems that the waves move randomly this way and that, the wind direction not really having any effect. I never played sh3 enough to compare it though. I figured its just another area where Ubisoft cut corners.
I'm less concerned with the visuals than with the mechanics being properly modeled. I remember with SHCE the graphics were very simple, of course, and there were only 3 sea states, but they had a big effect on your speed.
Perhaps, someone with knowlage of the ingame environmental details can comment.
