Most of the attacks are based on experience and previous knowledge of the ships in question. Nevertheless here are my "tricks"
Impact Pistols
Small Merchants (Passenger/Cargo. Small Freighters etc)
I set the running depth to 3m and aim just before the smoke stak. By hitting there you can either stop the ship from moving or explode the fuel bunker.
Small Tankers
Running depth set to 1m and aim a little bit ahead of the smoke stak (aft of the boat). If you hit the sweet spot you can blow up the fuel bunker and the whole ship in seconds.
Medium/Large Tankers
Running depth 1m aim just on the first mast (small bridge) from the bow. By hitting there the boat should sink in seconds.
Medium Cargo
Running depth 2.5m aim for the area between the last mast before the bridge and the smoke stak. It's a bit tricky but if you hit it properly you can break the ship in half.
Large Merchant
Running depth 1m and aim for the first mast from the bow. It should go down like a stone.
Empire Freighter
Running depth 1m and aim amidships. It takes a while but it will sink.
Destroyers
Whenever you hit them with a torpedo (running depth 1m) they should eventually go under
Battleships/Cruisers
Running depth 1m and aim for the gun turrets. The ammunition stored there should blow the ship up.
Magnetic pistols
Set the depth to 0.5-1m more than the draft of the boat, aim under the smoke stak or in the middle of the boat and fire. 9 times out of 10 you do break the back and she sinks.
Good Luck and Good Shooting