They were scrupulously counting torpedoes at least till Season 5
After which, they decided to retcon this and allowed more torpedoes to be manufactured using raw materials from the planets, allowing the use of over 90 of them by the end of the series
This article addresses the counts through Season 4: RICK KUZMA'S STAR TREK: VOYAGER STATISTICS. It discusses the uses, as well as a discrepancy that had Borg scanning the torpedoes in "Scorpion, Part II" and reported "32" instead of "13". Formatting and comments mine.
- They fired one torpedo in "The Cloud", leaving 37.
- They don't fire another one for almost a full year and then used three to drive off the Kazon in "Alliances"(34).
- Seven got used in "Dreadnought"(27),
- three in "Resolutions"(24)
- ... and then Michael Piller attempted to blunt our nitpicking good time in "Basics, Part I". Three torpedoes were fired at one Kazon ship and then "torpedoes" were fired in dispersal pattern Sierra at another ship. If you'll remember, we were taught at the Academy that the Sierra pattern requires five torpedoes but if you're going to sit in the big chair you learn to improvise. So season two ended with Voyager having no more than 19 torpedoes.
... Stay tuned because we will be vindicated in "Year Of Hell."
After all that bingeing, they got through most of 2373 on their negotiation and phaser skills until "Rise" when we saw one torpedo fired at a mechanical asteroid. ... at the end of season three there were n.m.t. 18 torpedoes left.
Speaking of the writing staff - season four started with Messrs. Braga and Menosky recalculating several numbers that are dear to nitpickers hearts, the number of torpedoes onboard being one of them
Voyager did not have thirty-two torpedoes at the start of the fourth season. If a Borg scan of Voyager showed 32, then there are some large holes in Borg technology. There were still n.m.t. 18
Five were fired in "Scorpion, Part II", leaving n.m.t. 13.
In "Year Of Hell", we were told that there were 11 torpedoes left. Taking into account dispersal pattern Sierra from "Basics, Part I" and other iffy situations, a difference of two is an acceptable variance. Now - if they really did have 32 in "Scorpion, Part II" and fired 5, that would leave 27. If there were 11 left in "Year Of Hell", how did they squander 16 torpedoes? But I digress.
- They used 4 as mines in that episode ("Year Of Hell"), leaving exactly 7. But that was alternate reality, so after that episode, 11 are left again.
Now, in actuality, in all the seasons, more torpedoes were used. this is what Memory Alpha has to say:
According to the Star Trek Voyager Technical Guide Version 1.0:
...An Intrepid-class ship didn't carry the material to fabricate casings for these torpedoes, and needed planetary raw materials to make new ones.
This would solve the inconsistency problem of the Voyager using over ninety torpedoes during the run of the series, while it was stated in the first season episode "The Cloud" that there was no way to replace the 38 torpedoes they had left at that time.
UPDATE: As per Izkata's helpful link in the comments, the rest of the series was counted as well after S4:
- Year of Hell I
Day 32: 11 torpedoes left, 4 used in next attack But: alternate reality, so it doesn't count. 11 left.
- The Omega Directive
One torpedo modified and fired. 10 left
1 photon torpedo used as "warp flare", 10 (or more) fired at the Malon freighter, 3 to collapse the entrance to the vortex. DING-DONG, we are in negative torpedo count territory!
- In the Flesh
19 (normal) torrpedoes and 10 class-3 torpedoes were modified with nanoprobes, so this sets a minimum on the number that was still available (29). This contradicts the count in Scorpion II
- Dark Frontier
So many torpedoes were fired that is is hard to count. And what is the point, it is now very obvious that the count isn't consistent any more.