I wonder if you did something dirty, because I have serious performance issues throughout the game since my last run to the point I don't want to play anymore - and all I did was to remove Roider Union, reinstalled Starsector to get 0.97a and added your mods.
This is certainly not reassuring as it looks like something unfinished.
So could it be a 0.97a thing or something in your mod?
I had to figure out why it was showing up, sometimes I forget what it's like without the Nexerelin mod. Normally it would have auto hidden that, it's a faction that can be joined through another mod to give you all the XIII ship blueprints right off the bat. That did give me a pointer that I have to hide that one for vanilla players.
As for performance issues, this mod has three modules.
The mod for blueprints only make it so some ships and equipment can be salvaged.
For the player faction mod, it's a lightweight mod that changes the names of fleets, titles, ui color, player allied fleet dialogue, and reveals your faction in the intel screen. It doesn't spawn a faction either and there are no added scripts so while I can't rule out the possibility, I can't really see what could cause it.
The XIII ships adds a hullmod, a starting faction profile for another mod, ships and fighters.
All three of the modules are extremely lightweight, should be with low overhead unless I'm missing something.