McCoy seems to honestly believe in a distinction between "real" and "unreal" rubies... And it doesn't seem as if he's pondering whether these things are figments of his imagination.
Does this mean that there still is value in "genuine" gemstones? Well, Kirk certainly seems to think so, when discovering the diamonds in "Arena"! Plus, "gem" is still synonymous with "valuable" for him in a certain episode with a suggestive title.
Why he would say otherwise in this episode is pretty obvious, too. He doesn't just want to indicate that he can't be bought - he wants to thoroughly humiliate his enemies for even suggesting such a thing. A little lie won't hurt him, but hopefully will hurt Korob.