New player here!
I have to give my input on this, after a few weeks of playing this wonderful game. So far, I've had great success using magnetic detonation and firing from DIRECTLY behind my intended target. Obviously, the margin for error is very small, but if you're certain the ship won't make any sudden turns (and the sea is not too rough), the chance for a detonation is very high. On several occassions I've managed to destroy the ship's rudder and propellers this way, which makes even a warship useless. If the first blast is not enough to sink it by itself, you can take all the time in the world to line up for a 90 degree impact shot. And merchants disabled this way seems to be abandoned by their convoys, which means that you can leave it where it is and come back later to blast it with the deck gun.