I doubt replication of antimatter would ever be much of an issue. You probably can't run a replicator unless you have antimatter to fire it up in the first place... In which case it makes no sense to replicate the stuff, even though replicators apparently can
create anything and everything. (However, there's TNG "Survivors" where the Uxbridges receive a portable replicator the size of a dishwasher, and don't appear to receive a lifetime supply of antimatter to accompany it...)
Starships would have plenty of antimatter in their main fuel tanks for arming the torpedoes at the last possible moment. More probably, though, the antimatter would first go to storage pods next to the loaders (such as the pods around Deck 11 on Kirk's ship that got "buckled" when Klingon weapons slammed right next to Kirk's torpedo launcher in "Errand of Mercy"), and only then to the individual torpedoes. But the connection between the explosive material of torpedoes and the main fuel of starships makes it easy to understand why so many of the hero ships would have their big torpedo launchers right next to the main reactor...
We know that torpedo yield can be selected just before launch (we see this happen in episodes like "Redemption II"), and it stands to reason that this happens by injecting varying amounts of antimatter. Of course, there are other alternatives: perhaps the loader selects a suitable torpedo, with a suitable (pre-loaded) warhead, from the rack just before launch, or perhaps a standard amount of (pre-loaded) antimatter can be made to explode with varying yields by adjusting the intermix. But the non-pre-loaded model fits the same data, and would explain all sorts of things, such as the way torpedo warheads are stored in crates aboard DS9 in "Tribunal". In that episode, the warheads could be replaced with scrap metal without anybody noticing - an unlikely thing if the warheads were highly energetic devices even in storage.
Also, here's another vote for the torpedo glow being either from a hyperactive warp field - or from a similarly turned-to-eleven impulse drive. TNG era probes emit this fancy flame-like glow from their butt ends when accelerating; torpedoes could be doing the very same thing, only with 999% added fervor, so instead of a pseudo-flame we get this blinding glow.
Intriguing, BTW, how torpedoes are the weapon of choice in ST3:TSfS when the hero ship is crucially undercrewed. Is this a blow against the loaded-from-ship's-tanks theory (because there'd be too few crew to do the loading)? Or against the stored-pre-loaded theory (because the dialed-down ship would be incapable of safely storing high energy munitions)?