For repairs it's deceivingly simple:
you have NO control on what item to prioritize repairs, you will see a moving 'hammer' over the current repaired item, but there is no way to change it, the terrible thing is: you can actually change the hammer position and put it on another item, but it will return to the previous one when you close window and re-enter. This indicates that the process is bugged and therefore malfunctionning...
What you can do instead is to talk to the engineer and send a major number of crew doing repairs to accelerate them - or concentrate on the flooding; be sure to revert this order for better sub handling once important items are repaired (although it would be logical that all the sub handling like engine efficiency, engine speed output, turn rate etc. get REDUCED when a lot of crew members are busy with repairs, I was however not able to acertain that in my observations, so I still don't know exactly).
Low percent numbers in red means you cannot repair on sea and the equipment is not operable; other low (but not critically low) items take very long to repair.
Check if some crew in the crew management can be assigned more points to increase the repair quality and rate (I don't remember).
This aspect of the game is by far inferior to SH3 or SH4 where crew management is much better, but it's just my opinion that this factor should matter more.
Torpedos hitting ships but not sinking:
You will never get any credits or points for only damaged ships, so you always have to sink them. This means it's futile to attack big troop ships or warships when you have only something like 2 torps left...
After being hit, The ship must 'stay in sight', if the contact is lost (which means out of sight AND no sonar contact anymore by your sonarman) and then the ship gets hit and sinks you DO NOT get credits for it. This could happen when attacking ships in a convoy at long distance and then getting away too fast, the ships will be hit and sink but if the sonarman has lost their track then: no credits for you...Just use your chrono and get to halt somehwere until all torpedos get to target.
Then, unfortunately, if you damage ships in rough sea the ship can sink due to the weather - you DO NOT get credits even for that, so hurry up to 'finish' it with your canons or send another torp to 'technically' destroy the ship...
So how should you play? Just dismiss all this, if you don't get credited so what...It shouldn't change your strategy, I wouldn't just stay 'in sight' of a ship and risking getting killed by an escort for hunting the credits and points...In arcade gaming competition this is called BONUS LEECHING...
However, I would do a bigger effort for the case in rough seas.