We have never heard it categorically explicated that antimatter couldn't be replicated - but supposedly the power for replicators comes from antimatter, so it makes little sense to burn lots of it to create a little bit of it.
However, the torpedo warheads did not appear loaded. Or at least they probably wouldn't have been so carelessly demonstrated in the Cardassian court if they had the potential to blow not just the building but the city sky high. And they had been on long term storage aboard DS9, too.
Perhaps it's the supposed incredibly intricate forcefields that are the key component of an antimatter-holding warhead that give the biggest headache to a replicator? Food replicators might fall short on that area, even though we have seen them replicate functional weapons (a phaser in "Civil Defense", a transporter-equipped slug-thrower in "Field of Fire"). OTOH, a full industrial replicator might not be needed, as starships supposedly have the capacity to replicate their own torpedoes (the Voyager
faced a shortage when her replicators were down, but no longer faced a shortage in later seasons when her replicators were working again). Or does every starship capable of replenishing her own torpedo (and shuttlecraft!) supply come equipped with what amounts to an industrial replicator? I'm tempted to believe in an intermediate type of replicator instead.