I have no issues with the high restoration cost.
If restoring was really cheap then I would never use ships with D-mods and might even purposely buy cheap damaged ships just to restore them immediately which would remove the entire point of D-mods.
Involving resources or manufacturing output with restoration wouldn't make sense either. It would just make it more time consuming and meticulous hurdle while adding no real value to the game. You can already use the money generated by your colonies to restore ships if you want to.
The high restoration cost also makes sense lore-wise. If you badly crash your car or some home electronic breaks then you usually don't repair it. It's cheaper to buy a new car/appliance and the damaged one will be stripped for spare parts then baled (or shipped to some less picky 3rd world country). In the context of highly automated blueprint focused of industry of Starsector, similar practice seems likely.
Personally I mainly restored salvaged XIV Legions and other ships I couldn't produce or buy myself and also some cheap ships because I couldn't be bothered to find undamaged ones or wait for them to be manufactured. I chose to solve the problem with money rather than time and effort because I could afford it.
