You have to manually track them down. The code part of mutators reside in the KF/System folder.
But on the other hand-side, why do you care about them being listed in the menu? They won't affect progression or gameplay unless they were activated before.

I've got a feeling the files just haging around is somehow affecting KF's performance. I suffer framereate drops in stages with enviromental particle effects such as rain, snow, fog, smoke, etc., and I spend most of my time in Solo.

if you downloaded mods improve the graphics, it's files in the folder System, U., UCL. If u delete it ( mutators ) -The game will not see other files of mods, and will not "connect" them. Thats trash, files do not interfere with the game. f you are experiencing problems with FPS - delete files will not help you.
There's also a mods , what not add new files... They modify original ones. So, I advise you delete all new files in all folders ( other date change ) ,check the cache of KF and Steam will download automatically original files.. Sorry for bad english)