The Confederates reuse dud federal naval shells at Vicksburg for the same purpose. wouldn't Anderson have had plenty of such shells at his disposal which he couldn't have used because his guns faced out to sea? He wasn't expecting an assualt from the sea to the extent that he would have needed every such shell he had, was he?
We think of the Confederates as being desperate for muntions, but that certainly would not have been the case with Anderson at Fort Moultrie. What advantage would the usage of such improvised muntions as "Thunder-barrels" have given him? It certainly would have been a large explosion with a 60 gallon Hogshead barrel filled with powder. But that explosion would not have been under much force being contained only by the wooden barrel.
Since they were deployed as a defense, I can only think of it as being a "Flash" weapon intended on burning, and not necessarily killing, a large number of people in its reach.