Realistic? I don't know. My opinion is you should be able to man the flak guns in rougher seas than the deck gun, but how rough is too rough? Can't say. Maybe they could have made the cutoff point 7 or 8 m/s. There has to be a cutoff somewhere though, so I have no problem with it. I don't battle airplanes and I rarely use the deck gun so for me it's no big deal.
Yes, you will have gun weather at sea. It will happen, maybe not for a few patrols, just be patient. The weather is random, ya never know.