If it's 1942, as you say, running decks awash to attack a convoy is a very bad move. Remember the device known as RADAR? Yes, that disguised medieval torture device over there, on that PBY your crew didn't spot. It's also on many escort vessels, and they sure do have an eye for torturing you. Try attacking from one of the sides of the convoy and maneuver based on the escorts' maneuvers. Always keep a repair team available, if worse comes to worse you may need it.
RADAR: I'm on an aircraft, preparing to torture you.
U-boat commander: O rly?
RADAR: Ya rly.
*boooooom*
CE: We're taking damage sir!
CE: Hull damaged sir!
CE: We're taking damage sir!
CE: Diesel engines destroyed sir!
CE: Electric engines destroyed sir!
CE: Watch tower destroyed sir!
NA: Shut up will you?!
...
CE: Current depth 280 meters.
CE: Hull damaged sir!
U-boat commander: No wai!
Internet meme version of a 1944 aircraft attack.