The torpedo from Dark Frontier is an interesting case, to be sure. The lack of a glowy exterior again suggests that the glow doesn't have any direct connection to the casing at all, but is only present when the torpedo actually fires
. In that case the torpedo wouldn't have built up to a detonation so much as built up to the colossal (and uncontrolled, since there's no firing tube) discharge that tore the ship apart from the inside.
Why use a photon torpedo instead of, say, a tricobalt device or a demolition bomb? Could be just for convenience (they had plenty of torpedoes), but more likely because Seven of Nine had identified a critical component somewhere in the probe that couldn't be attacked from the outside and Voyager beamed a torpedo into the ship with its business end pointing directly at it.
Swapping warhead charges, though, is something to think about
: to what extent is a matter/antimatter reaction even useful as an anti-ship weapon? Shields and hull plating seem perfectly well suited for dissipating x-ray flashes, so the warhead would probably be in the form of something harder to repel; something similar to a phaser blast, but considerably more powerful.