FWIW, in DS9 "Tribunal", Cardassians and apparently Feds as well thought that the Maquis would be interested in stealing photon torpedo warheads straight from long term storage.
Doesn't necessarily mean they would be stored full of antimatter and ready to explode, though - possibly antimatter is trivially available, but devices that can reliably store it and then suddenly and precisely release it at the enemy are very difficult to manufacture, and therefore must be stolen?
I'd argue that the much-maligned warp core ejection systems of Starfleet vessels exist specifically for the reason discussed here. They are not very good at saving a starship from being destroyed - but they are very good at saving a destroyed starship from blowing up like a tiny supernova and wrecking all the friendly starships flying nearby in a tactical formation. It is thanks to these ejectors that we get wrecks of starships, rather than mere clouds of dust and gas!
Basically, I speculate that whenever the enemy hits a warp core, a torpedo loading and arming system, or a fuel tank, there are finite odds that an ejector system will whisk most of the antimatter to a safe distance, even though this very act will seriously damage the hosting ship and probably kill all its crew. Thus we get an impressive fireball that spews wreckage and spinning bodies, but not a blinding flash that wipes the scene clear of all matter.