I've also been frustrated by adverse weather situations. I don't often kill my target with a single torpedo, so I rely on the deck gun to give it the last little shove into its watery grave. Setting up the shot isn't normally a problem, but what do you do if your shot brings the boat to a standstill and you are sitting there off its port bow waiting for hours/days to see if it will sink? As far as I understand you can't use the deck gun when winds are above a certain speed. I guess you just get the best torpedo solution you can and hope to sink it on the first shot. If it doesn't go under then wait(hope) for the weather to clear up so you can finish him.
Personally I'm using NGT's variable weather fix found at
http://www.subsim.com/radioroom/showthread.php?t=177507 so the weather can change more often. Otherwise you might be sitting there for weeks waiting for the weather to clear up enough to sink the bad guy.