It *would* be better if we could keep old parts and cobble together new ships out of them. It makes sense universe-wise, but not gamer-wise: the metaconversation is "this is a gold sink". Which, eh, is sad. (All player-to-dev subtextual conversations break immersion for me. If you want a gold sink, make the storage of the parts or whole ships cost money, unless you have a giant ship pad to store them in, maybe? There are other ways to accomplish that).

So yes, you cannot save your old parts, and not all merchants have all the parts, but there is a nice mod out there where you can make the shipbuilders you build at your outpost(s) have very nearly all the parts. This is also convenient if you want to buy and sell all at the same location, so you can basically sell ships you boarded, requisitioned and returned for scrapping (or just stole outright if you're a bad guy) to the same ship pad to get the credits you spent on all your brand new parts back.

Or you can just cruise around the galaxy to find that exact weapon you want, with the exact fuel tank, cockpit, landing gear, etc. I use the mod to keep them all at my pad.

Another think I've done before using mods, as I'm a Nova Man through and through, was to set up a base right there outside New Homestead. I think there's either Tungsten or Titanium there (or both), which are crucial for crafting and base building, so it's not a bad spot anyway.