As it turns out, Activision and Bungie wanted the Ghost edition to be “truly limited,” as Destiny Product Management VP Dyron Beede told IGN:
The incredible demand for Ghost Edition has exceeded even our high expectations. We made as many as we could, and in collaboration with Bungie, we always wanted it to remain truly limited.
Asked about other retailers possibly cancelling pre-orders due to stock issues, Beede said, “Individual retailers have the best knowledge of whether any are still available at their store.”
So, the best thing to do is check your order to make sure it wasn’t cancelled.