Another update:
It looks like there is no easy foolproof way. Whenever you delete a variable you should get a warning if it is used.
I did a quick test in Business Objects v5.1.6 and I got a warning when I tried to manually delete a variable being used as part of another variable, which was used in a complex filter.
I did NOT get a warning if I tried to manually delete a variable being used as part of another variable which was used as a Master/Detail though!
Of course if you delete a variable that is used in the definition of another variable the menu Data| Variable… will show an exclamation mark.
Regarding used universe objects, see: List Objects Used in a set of Documents
Andreas 
(BOB member since 2002-06-20)