I am finding the "tougher" ships to be one of the more frustrating aspects of GWX, now that I've installed it.
I used to be able to one-shot C2 tankers all day long by hitting them right under the superstructure.
Now I don't give any ship more than 2 torpedoes, and half the time they never sink.
I figure since I only have 4 bow tubes that means on any given convoy run I will only be able to realistically attack 2 ships if I give each one 2 eels. If you're going to give any ship in the convoy THREE eels, then you basically are only attacking ONE ship in the whole convoy with any chance of sinking them. Might as well not attack convoys at all if you are going to go that route.
So when I make a convoy run I pick out to "big ships" and give both ofthem 2 eels each. Either they sink or they don't.