And then spend a year debugging it.
That's really the crux of it, except it's more like "a year, and then something like half your time going forward". Multithreading for *this* sort of thing makes the code way more complicated and bug-prone, and also makes the bugs much harder to reproduce, diagnose, and fix. Starsector does do multithreading for a few things where it's a good fit - namely, music streaming, and some tasks while loading the game - iirc sound decoding is done on another thread, as is the compilation of loose scripts by Janino.
Plus, using multiple cores helps more on the high end than it does on the low end (which is where more help is needed), so if I was going to put a lot of additional time into optimizing, I'd probably utilize it in other ways...
This causes stuttering after a half hour session.
Sounds like something (probably a mod) has a memory leak and the GC is "thrashing"
You could up your allocated memory and it'll take longer before the system gets in that state.
Yeah, that seems pretty likely! Some common kinds of mod-memory-leaks only ever double the required memory and don't keep growing beyond that, so increasing the allocated memory could actually resolve the issue entirely.