So, I don't have conclusive proof, but recently I've had stuttering, delays, and even one outright crash while saving after a long play-session*, and when I started a new game with Interstellar Imperium disabled (and otherwise the same set of mods), I've had no such problems - yet, at least.
It's entirely possible that II isn't at fault here, but the evidence is suggestive of a memory leak somewhere.
For reference, the other mods I'm running with are: Dassault-Mikoyan Engineering, Shadowyards, Diable Avionics, Outer Rim Alliance, and of course graphicslib and lazylib.
* I ran a test for this: when saving a game was slow and made the music stutter (but didn't crash outright), I then restarted starsector, reloaded the same save, and hit the save copy button; that second save was fast and without stuttering.