I always thought that while replicating a whole torpedo at once is not possible, since it is not possible to replicate antimatter, it would be quiet possible to replicate the components and then assemble the torpedo. Antimatter could be taken from the ships storage.
While this process is a viable possibility in an emergency situation, just like a ship being cut off from support for months to come, it seems not to be a energy efficient process. Also this would certainly drain the ship's antimatter storage very fast. First for the energy used in the replicating process and second if the torpedo is actually armed.
So it seems to be more effecive to store the missiles in advance.