Which always makes that episode where they've almost run out make very little sense.
At first glance yes, but not necessarily.
Space is vast after all - VOY was going along a specific route to the Alpha Quadrant, so it makes sense that they could have exhausted their Deuterium in between natural deposits.
Travelling all the time at Warp 6 or Warp 8 takes Deuterium, so does combat, repairs, daily needs, etc.
If VOY has a primitive AM generator onboard like the ENT-D (and it stands to reason it does), that would necessitate large amounts of Deuterium to be converted into Antimatter... which could exhaust their supply relatively quickly in between Deuterium deposits.
'Deadlock' was when the ship's AM reserves fell to LESS than 20% in that episode... BUT, the ship never struggled with Antimatter as such (or it wasn't much mentioned beyond that point)... only Deuterium.
According to the TNG TM, Starfleet is able to convert Deuterium into Antimatter in specialised solar facilities. I suspect the primitive AM generator would be doing the same thing, but it would require far larger quantities of Deuterium - so that gives us a reasonable explanation behind why VOY was struggling with Deuterium (but not Antimatter) - because they were expending it not just as fuel, but also as a method to produce more Antimatter (which also explains how they manage to fire a lot more photon torpedoes vs what they originally started with).
Another explanation is they traded for Deuterium and/or Antimatter whenever possible - and once the ship was in a semi good position, all they'd need to do is replicate parts for the photon torpedoes, then inject the harvested Deuterium and (regenerated or traded) Antimatter at the last stage - which also explains why VOY had something 32 photons in Scorpion, even though prior to that point they should have been down to about 17 or less - since harnessing Deuterium and producing AM is a painstaking process, it stands to reason they could only produce them in smaller quantities over time - otherwise, the ship has enough space to store something like 100 or possibly 150 torpedoes.