I don't think the irreplaceable torpedoes idea was stupid in itself (I do agree the 9 year Ocampan life span was dumb though). But they should have thought things through before introducing it, and then have chosen to do one of the three following things:
1) Not use it at all, since it would put too many constraints on the stories (a bit like the warp 5 limitation idea in late TNG imposed too many limitations and therefore the problem was very quickly dismissed, circumvented or even ignored)
2) Use it but consistently follow through upon it, making the firing of a torpedo a special occasion, a one-in-a-season event (after all they couldn't know they'd be home in 7 seasons)
3) Address it at some point (trade with an alien race with comparable technology, or the VOY crew getting better and better at becoming self sufficient and producing what they need, and eventually build their own torpedo and shuttle production facilities)
All three could have been done very well, even 2) wouldn't have been particularly difficult - after all, phasers can be every bit as potent a weapon as the writer of the episode needs them to be. But they couldn't even be bothered to spend a few lines on 3).