Janeway: They may have photons to waste but we don't.
Also Janeway: Keep firing until you hit something.
I always assumed that was just a holdover from the first season when they were resource constrained and hadn't yet found any means to replenish their energy reserves. I would also assume they found sources of antimatter along the way to top up their reserves for warp and used some to make new photon torpedoes. AFAIK, the only components of those they couldn't replicate were the antimatter.
(This is disregarding the self-replicating mines from DS9 which were antimatter-based; no idea how Nog Rom pulled that off)
Some ships do have emergency antimatter generators per the TNG Technical Manual, but they're hideously energy-intensive to run--something like a 10:1 ratio of deuterium used for each unit of antimatter. They only make sense to run in the rare situation you absolutely need to warp to safety when you somehow have deuterium and a warp core but no antimatter.
But holodecks apparently have their own infinite power supply incompatible with any other Starfleet technology, so perhaps Voyager used the holodeck replicators to generate deuterium to run their antimatter generator whenever the Doctor isn't practicing his sermons.
Efficiency would be abysmal even by the normal standards of this process, but it beats walking back to the Alpha Quadrant.
The bigger issue is shuttlecraft. Technically, they could replicate shuttlecraft, but it would have expended a ton of replicator energy they claimed they didn't have. On the other hand, they somehow made two Delta Flyers.
Well, they obviously know how to make it, and expected to be stranded for the next 50 years. Also, it's essential for all kinds of life-saving machines.
So, obviously they would build some antimatter generator. The show just don't focus on it. What is a shame, because it could be a more interesting quest than half of the stuff that happens there.
Now that I think about it, are they ever shown hunting for antimatter? Every episode I recall mentions deuterium specifically. So yeah, I would guess they do have a way to generate antimatter on board (that's hopefully more efficient than the converters used on Galaxy-class ships).