I suspect what happened is that you stumbled upon a game break landmine at some point, and unless you can go back to a save point prior to that happening, it won't ever be right and you're just ****ed. And it could be anything. The minute shit gets wonky on me I go back to an earlier save and that generally cures it. I'm at level 77 in my current playthrough, have a bunch of settlements that are starting to get somewhat complex, and don't have any of the issues you're having. And I have tens of thousands of rounds of random ammo just as you do.
The shittiest part for me is that ship capturing is now completely broken, which is apparently a common problem. I don't know if it's just a high level thing, or a hidden landmine thing, but the enemy ships I encounter on planet surfaces no longer spawn crew or open. They land and just sit there, and that's that. So I already couldn't board and capture them in space and now I can't board and capture them on the ground. That sucks balls, because it's the single most fun part of the game.
I still haven't loaded any mods yet, but I suspect the answer lies there.
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