1 - If you have "no dud torpedoes" selected, you shouldn't have any duds at all. Even with it selected, by mid 43 the duds should be getting less and less. Try going into the clock on the top of the book case at the left side of the captains office and re-check your gameplay settings.
2 - As long as you sink ships and keep taking new boats when offered, you shouldn't be retired.
3 - You will not get a choice to reassign every time. When you do get and choose the option, your first patrol from the new port will be in your old patrol area.
4 - There are no submarines in the target recognition manual that I know of. I have sunk enemy subs at sea with like 4 torpedo hits and yet some times I do not get credit for them. Not sure why that happens.
5 - The torpedo strength are the same if you use the same type. It depends on where you hit the target, I believe there are certain damage sections on the target, such as hitting a magazine. It's good to hit the merchants under the stacks (at least for me). Merchants have different cargo loadouts even though they are the same class ship. Some tankers may be empty while others are loaded with aviation fuel.
Donna