Imagine trying to do some complex task while skateboarding on a cobbled street in a rainstorm.
Now do that same task, on the same road, while riding a bus.
That's why ships can fire and subs can't.
Even in moderate weather where I could get the gun crew on deck, but the waves were rolling pretty decent, or at least in a harmonic with the boats motion, accuracy was almost nil. Some shots would sail 100's of m's over the ship, while others would plunk just a few meters from the u-boat.
But the ability to use the Flak guns in all weather is a different story. Especially for the guns up on the Turm. I recently sank a sloop with my flak gun in my IIa, then a day later, encountered another sloop, but in bad weather. So I rammed it. I didn't get credit because the wave action of pushing it under sank it.
.
But another thing a lot of players do is if they can't get gun crews on deck, they won't reload externals.