Welcome aboard Snordin!
Some merchants are armed from day one of the war. So it's best to check them out before engaging on the surface. If they do have a gun (just the one!) you can try and position yourself in the blind sport either ahead of behind the vessel your trying to sink. Remember that as the war goes on more ships will be armed, so the chance of you useing your deck gun on anything bigger than a fishing boat get smaller!
With sinking fast freighters, aim around the fore mast on impact seem to do the best in sinking them, they will not sink straight away, but then you can get away with sinking them with around two torpedos
Good luck and good hunting!