I'm not playing right now but some patches ago (january/february 2021) it was better not to repair them. You want to repair only the flying systems just to bring them to a station.
If they haven't change the behaviour it's more convenient this way
The tier of modulsmodules, etc. should be linked to the ship tier. If you scrap a tier S ship, it's more probable to find high tier rewards, so if you want better modules you have to scrap high tier ships