Welcome aboard to the light side!
I never heard of downloads being disabled. Try it again. If you have still trouble, Neal can help.
There's a lot of issues with 1.4. Most of us have upgraded to the u-boat add-on. It upgrades to version 1.5 and corrects a lot of the issues. You can still find mods for 1.4, but it's difficult. Almost all the mods have been written or upgraded for 1.5.
When you say "reload", what do you mean? Is it reload the tubes from the reserves, or what the game calls "refuel/refit?" If reload the tubes from the reserves, I don't have an answer for you. If it's the refit, then the game gives you what you started out with from your home port.
About ship sinking, the stock damage model is strange, there are mods that fix that. Don't try to compare damage from one target to another or one game to another. There are too many variables to consider. The class of ship, where the torpedo or shell hit, the skill level of the AI crew.
There is an option to upgrade boats as your career progresses.