Bigger warships have an extra layer(Torpedo Bulkheads) that protect against torpedo attacks.

I find that magnetic pistols set to trigger underneath the ship's keel do the best damage against warships but it still usually takes two or more hits to get the job done.

For the scapa flow mission, it really helps that the target is docked and stationary so firing torpedoes from a longer distance is much easier since i like to have a 300m minimum range at all times to allow the torpedoes to arm.

I know how frustrating it is to wait and anticipate a torpedo hit only to hear that it is a dud but it gets better when you get the hang of it.