Welcome aboard!
Yes, it really can be that bad, which is why they have lighthouses, lightships and foghorns. This is also why submarines tend to operate submerged during storms. As they said in
Das Boot, you can hear a lot further submerged than you can see surfaced.
There are problems with magical destroyers, though, even in the stock game, who can see you when they shouldn't. On the other hand, if it's 1942 most of them have radar.
This brings up a question: Were you operating off the coast at the time, looking for the enemy, or were you in transit, i.e. in the middle of the ocean? If the latter, it shouldn't have happened. If the former, then you should ride out the storm