I don't see the objection here. We have seen torpedo yields vary from "flash-bang" to "geography-rearranging grapnel of Tsar Bombas"...
That's just it: when have we ever SEEN that high-yield Tsar Bomba setting? It's mentioned in dialog from time to time, but usually in boast, never in an actual technical discussion.
furthermore, dialogue has established that the yield indeed is variable. No type of torpedo explosion should surprise us in the slightest.
Except that for the kinds of detonations we USUALLY see, we'd be looking at a torpedo primed with not more than a couple of miligrams of antimatter; the torpedo would actually do more damage if it dumped the antimatter into thrust and just RAMMED its target at near-orbital velocities.
There's also the fact that torpedoes don't seem to be visually more impressive than some of their more exotic non-antimatter counterparts; in most cases, photonic torpedoes aren't VISIBLY more powerful than spatial torpedoes, for example, they just move a lot faster and are more effective against shields. The Narada's torpedoes aren't stated to use antimatter either, and yet they seem to be implied as being relatively powerful, possibly moreso than torpedoes, and in Nero's case there's no specific reason for him to set them to a lower yield than they could otherwise achieve. There's the Krenim transphasic torpedoes which are devastating against Voyager only because they can slip through shields like they're not even there, but when one of them detonates INSIDE THE HULL, it is a far far cry from a thermonuclear explosion (and the Krenim, being the assholes that they are, have no reason at all to dial their yields down for humanitarian reasons).
More importantly, we've seen what an actual nuclear-scale blast does to a starship, as in Balance of Terror where a Romulan warhead detonates a hundred meters away from the ship. The effect of this warhead is totally unlike ANYTHING we ever see from photon torpedoes and is a jarring contrast with even TUC, where the ship is hit by upwards of a dozen photon torpedoes that could only have been set to maximum yield (and one physically blows right through the hull, laughing at the shields on its way through).
Canonically, an unshielded starship hit by a quarter kiloton blast winds loosing a pretty enormous chunk of its hull
. Even maximum-yield photon torpedoes rarely do this kind of damage on their own, which sort of puts an upper limit on their yield IMO.