I am not a mod designer, but I do not think what you are asking is possible. Or at least, I have never seen any mods which enable what you are requesting.
It may be there are mods which limit the amount of damage, but I have never seen one which makes the torpedoes hit or takes away the ammunition of the ships. Within the game you can set certain options which will help you, like not selecting the "dud torpedo" option.
I am afraid you are simply going to have to learn how to play the game "properly." If you are missing with your torpedoes it is because you are making improper attacks. In the sticky threads at the top of the forum, you will find links to guides which will help the new player understand the game.
Getting killed frequently by the escorts/destroyers means you are doing things that allow them to see you and attack you or hear you and attack you. Staying surfaced while close to enemy ships will get you sighted, as will other behaviours such as running your engines quickly underwater or staying close to the surface when close to escorts/destroyers which can hear your or detect you with their gear.
The tactics and strategy guides will give you ideas of how to accomplish your goals while minimizing reducing the chances you will be seen, heard and attacked. I visualize playing this game as being similar to hunting wild animals. You have to understand how they detect you, how you have to quietly and stealthily approach them and not be too loud and aggressive when you approach, or stay quiet and unseen while they approach you.
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