I will assume we're all familiar with one of the popular gripes/issues with Voyager and no, for once - it's not a Tuvix thread.
Today we're defending the torpedo/shuttle count.
In many of the discussions on this topic (especially regarding the torpedoes) key context is often ignored or otherwise not mentioned.
So let's start with said Torpedoes.
The line about Voyager not being able to replace their 38 (of a total 123 fired over the series) torpedoes once they're gone was in 'The Cloud', the fifth episode of the series.
At this point in the series Janeway was (as established in the conversation about Torres' Starfleet procedure breaching dilithium refinery in the previous episode) reluctant to step outside of Starfleet procedures. Especially I would imagine for the purposes of replicating antimatter based weaponry for obvious explosion related reasons.
Voyager was also hesitant to trade technology at this stage, a policy that clearly was relaxed as the truly dire reality of their situation was realised - evidenced by them giving holo technology to the Hirogen amongst various other trades (successful, or attempted as was the case with the Malon).
From Voyager's perspective at this stage also the major races they had encountered in the Delta Quadrant were either primative, or wanted to steal organs. Neither making for great allies. Janeway was likely also conscious that they could stumble into borg space at any moment and so would want to conserve their munitions as much as possible.
We see a number of 'Voyager trades with people' episodes as the show goes on and the most relevant one here is the (otherwise shameful) episode Retrospect where Voyager is seen actively trading and shopping for weapons.
With this context, it's easy to see how the torpedoes ended up being replenished despite the line in episode 5. They traded for the raw materials or components and built them.
As for shuttles, they literally built the Delta Flyer - a highly experimental Tom Paris napkin scribble of a design within a week. Then blew it up and built it again with even more experimental technology.
They clearly had a lot of practice (re) building shuttles by season 5 to pull that off!
Yeah it's reasonable to assume that as the series went on the situation with energy and resources just became less dire as voyager found their footing in the delta quadrant as you've eloquently put. At the end of the day they have one of the most advanced federation science vessels in the fleet, replicators, and a crack team of engineers with nothing but time. The earlier caution was Janeway rightfully being overly conservative with her resources given the uncertainty of where they were traveling and the hostility of the space they landed in.
Aside from that, it just makes for a better story. They wouldn't want to hamstring their ability to write action scenes because of some line from the first season.