Not sure what/how CCleaner does/works, but if it does something like cleaning cookies, it has to access places.sqlite. Similarly no reason that it couldn't access prefs.js, though I would (hope) that to be unlikely?
Imagine they have forums, & settings within the program itself to determine what is or what is not "cleaned".
Imagine they have forums, & settings within the program itself to determine what is or what is not "cleaned".