I don't know whether it's a good idea, but maybe one could solve the 'high-waves in port' problem with a work-around based on sea depth
Basically, the idea would be to limit the wind speed to < 4m/s if the water depth is, let's say, < 10m. This might be problematic with harbor raiding, but... Anyway, it's just an idea to remove the unrealistically high waves in harbors.
Regards, LGN1