It could be that the torpedo hit the hull at a less than optimal angle. Even at 90° AOB the torpedo could have hit the lower part of the hull which is curved, happens to me quite often when the seas are rough. In storms I usually use magnetic pistol and set the running depth to about 1.5 meters below the keel to compensate for waves. Attacking in a storm is not optimal anyway, so that's the best you can do really.
Ship damage depends on the cargo it was carrying, at least in WAC hitting an ammo freighter or a tanker with one torpedo is usually devastating, compared to big cargo ships carrying non-volatile freight, which usually require 2 fish. It is often a good idea to aim under the smokestacks, that's where the engine room is. Even if the ship doesn't sink it will stop dead in the water, easy target for another eel or your deck gun.
Oh, and welcome to SubSim
