Since Spock was describing damage to the ship, I never thought he was talking about anything BUT the ship's warp drive antimatter supply.
That would drive a somewhat frivolous wedge between Spock's two sentences, the first of which establishes the decks he is concerned about. More significantly, we saw where the Klingons hit our heroes - on the underside of the saucer, not at the nacelles. It would take unnecessary effort to postulate "further hits" or "unrelated sentences in the report"...
1) Starships typically fire torpedoes from a small number of sophisticated, fixed-position launchers. They are almost always fired one or two at a time, rarely in salvos.
This might go well with the idea that torpedoes are "command-guided" or "semi-active" and can achieve nothing if the ship that fired them does not provide constant support of some sort.
It might not be limited to guidance, even. Perhaps torpedoes indeed are "aphysical" blobs of plasma that are both propelled/guided and held together by a subspace field projected from the mothership - and the Romulan plasma weapon is simply the same thing in a larger scale? That is, perhaps the physical casing evaporates at launch (but can also be used in non-evaporating applications such as probes).
This doesn't go well with the fact that we sometimes see glowing balls of fire emerge from a launcher yet a physical projectile very definitely reaches the destination: Spock's coffin and the dud torpedo from "Starship Down" are examples of this. Also, some torps are described in rather blatant plot terms as fire-and-forget weapons. All we are missing is a clear case of a ship being destroyed after launching a torp, yet the torp continuing to pursue its target... But since this is such a cinematic classic, I wouldn't bet against a future movie or episode featuring such a scene.
The piecemeal firing might thus best be taken as a case of the projectiles (or actually their antimatter warheads) being expensive rather than expendable. For the same reason, ships bristling with dozens of missiles today don't ripple fire; two missiles per target is already the sign of desperate priority expenditure.
2) Torpedoes apparently require a considerable amount of power to use, since even Federation vessels like Defiant cannot fire them while cloaked and sometimes they cannot be used at all during low-power conditions.
Might just be that when primed, they
radiate considerable power, which not only has to be compensated for from the ship's supplies until the very launch, but will shine through most cloaks.
3) Torpedoes do not always (or even usually) explode when they hit things; they sometimes "splash" against a target, flattening out and then disappearing altogether. This is especially the case when torpedoes hit shields. It actually appears that the torpedoes THEMSELVES do not explode, but merely cause things they hit to deflagrate on contact.
This might speak more of the shields than of the weapons deployed against them. And the shields must have some pretty magical "disappearing tricks" up their subspace sleeves anyway, because otherwise the "secondary" effects of an otherwise "deflected" shot would no doubt be lethal in themselves - transfer of momentum, release of energy into the shields thus necessitating its further release
from the shields somewhere else, etc.
Also of note is that hits by decidedly non-projectile weapons against shields cause "gasoline explosions", in DS9 and VOY and ENT at least, but also to some degree in TOS and TNG as well. These "glowing balls of fire"/"flashes of light" may hide the fact that an actual antimatter explosion from a properly detonating torpedo is in fact a singularly unimpressive and often completely invisible, well, sight. Which it in reality might well be.
4) Phasers can be used to shoot down missiles, rockets, fighters, shuttlecraft, even regular-ass normal torpedoes. But not, for some reason, PHOTON torpedoes.
Even in the oddly scaled visuals of Star Trek, photon torpedoes are significantly faster than the other objects quoted. That didn't stop Kirk from ordering a torpedo to be targeted in ST2:TWoK, though - and in a point-blank situation where a modern CIWS system would have real difficulty coping.
it could be that photonic torpedoes are really just a type of extremely unsafe hologram
Nothing against this cool idea as such. But see above.
Timo Saloniemi