There are a couple of ways to fix that. The problem is that the computers that SH3 was built for couldn't handle the graphics of extreme seas. The other problem is that it was easier for them not to worry about ships sinking in heavy weather if there isn't any heavy weather.
Along the way people tried to modify the weather to get heavier, and it couldn't be done. One cool solution was to double the wave size for the listed weather, making it look like it was twice as strong. One of the variations of this is built into SH3 Commander, allowing you to adjust the way the waves look, even offering a variable option according to the season.
But you asked about the guns. The only real fix is to go into your SH3/Data/Submarine folder and select the type of u-boat you're using. The second file in the list should be the cfg file, which opens with NotePad. At the bottom of the [Properties] list is the StormConditions. The max wind speed is set for 7 and the rain intensity is set for 0.1. You can adjust those to anything you like (max possible wind is 15 and rain is 1).
Or you can use GWX, which has already adjusted those somewhat. I have mine set to different speeds for different boats, and judge whether I use the gun by whether waves are washing over the deck (I do use Commander's 'Seasonal' Wave Height settings).
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