Hello
first of all you should have installed GW on a 1.4 patched version of SH3. If the game isn't patched I don't know what will happen.
Now on the subject of the C2 Cargo. GW is using a different damage system than the original game. Ships can be sunk by flooding or by explosions. Try to hit them in different compartments. See this thread it might be of use to you
http://www.communitymanuals.com/shii...hip_Weak_Spots
When you're using the deck gun try to aim below the waterline. That way water will enter the boat and lead to eventual sinking of it. In GW you will need significantly more rounds to sink a ship than in the original game, so don't worry about it. It's something normal.
I hope this helps you a bit, and if you need anything else I'm sure everyone here will be happy to help you.
Good Luck and Good Hunting