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.

This is unfortunately a loosing battle. I've been explaining how it makes perfect sense for years, but as soon as another person starts their voyager rewatch, another thread pops up about how they said they can't replace torpedos, and others jump on board to call it a plot hole.

It is indeed all about trade, but it's really about one specific thing: antimatter. Three things are required to keep the ship running almost indefinitely: antimatter, dilithium, and deuterium. With those things they can manufacture all the parts they need and keep the ship, shuttles, and torpedos flying. Dilithium can be mined and processed using the refinery that b'elanna built from the secondary impulse reactor. Deuterium can be collected in space or extracted from sea water. But antimatter takes massive infrastructure and energy to produce.

In the beginning, they weren't sure if there would be any opportunities to acquire more antimatter, and without it they're boned, in both torpedo/shuttle production and ship propulsion. But they soon found out that the delta quadrant was just a big flea market filled with warp capable races. And yes, there may have been a moral/procedural issue in theory, but i'm pretty sure Janeway would have traded with the bad guys if it came down to the ship not being able to fly anymore.

So after they realized they can get more antimatter just about anywhere, there were no more issues at all. They just had to plan things out to make sure they wouldn't run out in the middle of a void or something. It would have been nice for someone to mention it directly on-screen, but they didn't and here we are, so we just have to keep fighting the good fight for the benefit of all.

of a total 123 fired over the series

Here's a video for anyone wanting to count.

Yeah, showing that Janeway was willing to trade with arms dealers was the best thing to come out of "Retrospect," which is the faintest of faint praise.

I do wish there was more clarity on exactly what can and cannot be replicated, and how much it "costs" to do so, but that's a franchise-wide issue.

Chakotay also says in “Alice” that they have a full complement of shuttles, so they definitely had sustainable manufacturing capabilities eventually.

Would have been nice to have gotten at least a vague reference to it over seven seasons, though…