There's no need to bottom-out your boat, unless you're in broad daylight, which is not the best time to raid a harbor. Enter during the night through the narrowest point at slightly below "decks awash" and once you're safely past any potential shore batteries, return to "decks awash" to conserve batteries. When approaching your targets, return to "decks awash" to reduce your chances of being spotted. Don't worry about the star shells, just stay focused on your targets.
Your torps should be fine down to the depths (keel) of your target, unless of course, there's a shallow land obstruction between you and the target. In that case, just adjust your point of attack.
On the other hand, if you have "Dud Torpedoes" selected, you may also be experiencing premature detonation or faulty depth settings. In that case, you just have to live with it until the problems with the torps are ironed out, in late 1943 (
I think).
Oh yeah, one more thing:
