Okay, going with the replicated anitmatter theory... I have a question or two.
If replicators work on the theory of
matter-energy conversion (á la the transporters and holodecks), then how are the appropriate anti-particles synthesised? You can get antimatter particles through various particle interactions, but there's a certain amount of "wastage" with this process - electron/positron pairs, high-energy gamma rays, etc, so the yield isn't going to be 100% of the replicator material converted (as mentioned by
Timo previously), though I will concede, there's nothing to say there isn't some from of wastage with normal matter replication, but I doubt it would be on the same scale. But I'm not convinced you could synthesise enough "pure" antimatter through this method.
[Just an aside, to be überpicky (sorry!): I don't think it's right to say a ship or its systems are run on antimatter, rather the energy produced by the matter/antimatter reaction. Running anything on antimatter alone would probably destroy the ship and a good deal of the surrounding space too

]
Assuming that you do get a decent amount of antimatter, in most (I'll take a leap of faith here and say
all) instances of seeing the replicator in action, the object has always appeared on the replicator "pad". Now, given the nature of anitmatter, if it is replicated and comes into contact with the replicator, surely the whole thing is going to annihilate itself in your face, or at the very least give you a lethal dose of gamma radiation.
Or could a possible solution be to set up said replicator behind a forcefield using some carefully manipulated magnetic fields?
If that's the case, I'm not convinced that replicating the antimatter is the best way to keep energy expenditure at a minimum, as would be the case on Voyager at least some of the time... Which could bring us back to the initial comment that maybe replicating torpedoes was not impossible, but was too energy expensive.
Just my two pennies
Regarding warp cores for shuttles: True, they are quite small (if the Delta Flyer's core is anything to go by), but to have them sitting in storage? Would it be possible to have a shelf of matter/antimatter reactors without their reactions becoming a problem? Would it even be considered safe enough? In any case, considering the amount of punishment Voyager seems to have inflicted on it, I wouldn't like to be the guy assigned to keeping an eye on it