In harbours a limit to 2-3 feet is definitely enough. I have never seen waves higher than approx. 1 meter/3feet behind wave breakers.
But I have noticed, that in a tutorial video about ShipSim Pro (on YouTube) the waves can be set to be high outside the mole, and are low inside the mole, which looks very realistic. You can sail from a stormy sea into the shelter of a harbour in the same environment! Great! I hope we will find such features in SSEx, too.
In SS08 e.g. in Marseilles, the waves are limited in the entire environment.