For what it's worth, I brought my old stock catted h-pipe to an auto recycler locally & they gave me $150 ($60 each for the larger cats & $15 each for the pre-cats)for it. The cats are what they're after, like AlsCobra said, there are precious metals in there. I bought a used stock h-pipe for an '89 GT for $50, took it there and sold it for $100.
Did you have it noted in the work order "Customer wants to keep all stock parts"?

Chances are they got $$ for the cats & if another "stock exhaust" comes in, chances are they'll do the same thing