So...about 5ish years ago, I worked in a GC. I did work the door here and there before I got into operations/warehouse/inventory positions(and quit selling gear). I must say, they do that because half of the salespeople are retarded. No joke. You walk out the door with a mismatched serial number, good luck getting warranty repair anywhere. Seriously, I've dealt with authorized repair centers forever, and they will seriously give you the hardest time ever if anything doesn't match up with their records...and your proof of receipt w/matching numbers of course.
Oh yeah, I don't usually defend the bastards, but, they really aren't profiling anybody for theft, you'd be pissed if you checked your bag later and were missing some strings...it avoids complicated customer situations.
Also, inventory control/management does help with pricing and making sure that a store that has tons of stuff it can't sell quick enough is able to provide it once they've promised it to you.
...I only caught one person trying to replace a guitar in their case ever.
...it cracked everybody up...good times....