Isn't the fact that Voyager was only outfitted with 32 torpedoes a sign that it wasn't really intended for war. Or was that only because they weren't fully equipped?
Either way I think it makes more sense to assume Voyager is less powerful than the massive E-D. I think that was supposed to be part of the point of Voyager, a smaller weaker vessel trapped all alone in the Delta Quadrant. And hey If the Galaxy is eclipsed by almost everything the Feds built within less than a decade, well that just seems kinda sad.
The reason voyager was outfitted with 'only' 32 torpedoes was because it was just launched and sent on a 2 week mission to retrieve a smaller Maqui raider (probably as a 'shakedown' mission in the first place).
It explains both the low torpedo count (because it's physically STUPID to outfit a vessel of THAT size with only 32 torpedoes, when realistically, it would be able to hold AT LEAST 4x as much) and low count of supplies on board.
SF was not expecting something like the Caretaker to occur, and Janeway was placed in a situation where she had to either possibly risk sacrificing the Ocampa for the purpose of getting home faster, or destroy the array and find an alternative route home that wasn't at the expense of an alien culture while preventing a technologically superior installation to alter the balance of power in the quadrant in favour of a race that might have likely destroyed most in it's path.
Also, taking into account 24th century technology overall, each SF ship would have the ability to sustain itself and resupply using any form of raw materials (given their ability to transform matter into energy or energy into matter).
Shuttles were mostly retrieved and/or repaired after a rather unpleasant barrage with the aid of replicators (in systems that contain any kind of raw matter or simply asteroids rich in 'standard' composition that could provide tons of energy or materials when converted into one or another) or simply were replicated in pieces and then assembled.
Torpedoes can be replicated in parts to be later on assembled, with anti-matter being the only thing they apparently cannot replicate as easily.
However, if they spend say a week in a system using raw materials to resupply themselves, then they would probably be able to modify existing systems on-board for anti-matter replication.
Or they could simply find alternative sources such as omicron particles that would be used to boost anti-matter reserves (quite possibly, other substances exist that can be used to do the same thing - and I would surmise they convert this substance into anti-matter utilizing the Warp core or systems that work with anti-matter in general)
