On multiplayer there seems to be a desync between what the weather map and the wave visuals are showing and the buoyancy calculation. We have ships that fly and get fully submerged by invisible weather/waves. I have seen reports that also some packet loss (hitches) are being experienced during this time and also experienced this myself.
Why I say it's only the vehicle and wave interaction buoyancy-wise is that the screws do spin up if they clear the water and when you get submerged the engines are not getting air.
So only the rocking of the ship is not right. The waves that are displayed do interact with fluid ports and propellers, they also are the same as is displayed on the weather map, however the rocking of the ship seems to happen on another set of desynched waves.