How the Silurians Voth ended up out there is also a bit wild. Sure, one day Earth geologists will find something via seismic scanners and go "Hey, George, come here, this rocks!" like they do for detecting oil deep underground, but even if a Voth civilization existed to the point they all flew away with their developed technology... Chakotay's heart was still in the right place and it's a charming theory... but all the way to the Delta quadrant still seems sketchy.
I enjoyed that episode, and the lack of evidence of a Voth culture on Earth can be easily explained by plate tectonics. The remains of their civilization is buried so far below the surface that it would be risky to impossible to try digging any of it up.
Besides... when you look at the basic plot elements, it's a retelling of the Galileo story. Scientist finds evidence that leads him to a theory that clashes with current religious doctrine. Scientist is sufficiently threatened with all kinds of dire consequences and forced to recant his theory if he wants any sort of tolerable life in the time remaining.
Of course the Voth scientist was more fortunate than Galileo... he wasn't put under house arrest and he hadn't gone blind (which Galileo did from doing too many observations of sunspots through his telescope).
It's been established that Voyager could have solved three of its worst inconsistencies (infinite torpedoes, unlimited shuttlecraft, and Harry's rank) with one scene, maybe a minute or so in duration. They didn't care enough to do even that small bit of footage. The showrunners had gotten completely sloppy, and clearly had no regard for the intelligence of their audience. So, if they thought something would make a good episode, they went with it, screw realism.
Something I came up with many years ago when our local Star Trek club designed our own ship was that we'd gotten hold of the Kelvan technology that turns people into little styrofoam dodecahedrons... and modified it for non-organic things.
If our 23rd-century crew could do that, just think what would be possible in the 24th century. Janeway actually had several supply closets
stuffed with shuttles and torpedoes that were in the form of little styrofoam dodecahedrons. When she needed another one, they'd just pick it up from the supply closet, push a button to return it to its original form, and boom. Problem solved.
Or at least
that problem was solved. Somehow they mucked everything up when modifying the technology for complex machines. It never again functioned with organic matter. This explains why Voyager needed to stop off to do hunter/gatherer stuff on dangerous planets or shop at the nearest farmer's market when they needed to replenish their food supplies.
Umm, the inconsistency always was finite torpedoes and limited shuttlecraft. No other starship in history suffered from such things - so why would Janeway's, all of a sudden?
I dunno... maybe because they were 70,000 light-years from the nearest Federation starbase, so they had to make replacements themselves? It's not like they could pull in at the next Federation planet and say to them, "Chakotay crashed our last shuttlecraft past our ability to repair it, so I'm putting in a requisition for another half-dozen, and I need them
before next Tuesday."