Can a something.library file actually cause a crash even if it isn't in use?
Well, I hate to be like Bill Clinton... But that depends on your definition of "cause" and of "in use."
The presence of a library in LIBS: may be queried by a certain program, even if it doesn't plan on using it. IIRC, several CD32 games queried the existance of lowlevel.library, without actually using it. If it found a lowlevel.library, the game would assume it was on a CD32, and might crash an A1200. Thus, a library not in use COULD cause a crash of a badly written app. I suggest digging around with SnoopDOS to figure out what is really happening. :-)