When it comes to the big question, why is restore more expensive then buying/building a new ship, I have some thoughts.
Gameplay wise I suppose it is to put a cost to using and risking rarer ship types that can't be as easily reacquired in the early to mid game. Losing a Shade should be kinda costly when compared to a Lasher, because Lashers are easier to acquire. It sucks sure, and promotes save scumming but honestly any penalty does that and I'm not sure the game should be built around preventing reloading.
If the game is more built for an ironman, no reloading, experience then high restore costs for rare ships seems fine.
Thematically, what of common ships? Or ships that a local faction can produce, even if others can't? Sure getting the replacements parts to rebuild a Shade at a hegemony ports should be expensive, as it's not a blueprint they have or can easily produce even if they do as it's not in their doctrine. A Tri port should, however, find it far easier and it does make sense for you to be able to rebuy or restore their kinds of ships at their ports. With the cost being if you made an enemy of a faction that uses ships that you don't have the blueprints/industry for, and so can't replace or restore at your own ports either.
And the same goes for commonly usable ship types. It should never be expensive to restore a buffalo transport because everyone has access to them.
Ships like the Legion 14th should be expensive to restore as spare parts for a model of ship not produced, anywhere, have got to be expensive or risk having luddite artisans make them from scratch for a luddicrous amount.
Restore costs should be dependant on those factors I believe. Possibly even giving factions like the pirates to trade, say, a bulk of fleets (from time to time) to a single fully restored fleet for an elite pirate threat! Giving variance where it makes sense to do so. At that point a restore is more of a choice, as restoring is cheaper yes, but restoring some usless d-mod for hull integrity for a ship that never sees combat might still be more useful to the player for the savings.
The current fixed restore cost just encourages reloading early game, replacement mid game which is just wasteful considering the supposed thematic desperation of the times (throwing away Sunders, when you can 3d print them for cheaper, or thematically make 'creative' repairs seems absurd), and late game you have infinite money so the cost doesn't matter any more.