The mods looked sort of stupid to be honest. Some obviously didn't pay attention to lore either (one major mod adds a fishing skill when a common event mentions that fresh fish is impossible to find what would seem to imply the rivers have been messed up). Also silly combat moves like 'Bicycle Charge'.
That's an interesting interpretation! One thing I was trying to do in the game was to avoid over-exposition. I didn't want to fall into the "midichlorians" trap, nor did I want to paint myself into a corner by expressly forbidding something I later really wanted to do. (The NEO Scavenger lore is basically designed to let me play with the sci-fi/supernatural toys that I want in some cohesive way.) As such, we have hints and glimpses via headlines, files, and rumors. Sort-of "constellations" with which people can form their own interpretations.
The mass fish deaths were not intended to mean that all fish in the world died, though I could see why that might be how one reads it. Mass animal deaths are actually
more common than you'd think, even though we don't always know the cause. However, you're right that they can be disruptive (if not fatal) to local communities.
As for the mods, it's been a while since I've poked around in them. I've spent the most time in Kaaven's mini Mod of Doom, as I find his design sensibilities mirror my own more often than not. He's also been instrumental in balancing designs and suggesting tweaks to the game over the years. In many cases, his mods do things I really wanted to do but didn't have time for. And I think he does a pretty good job of keeping in line with canon. (Also check out his "Fields of Dead" mod, which adds more detail to decomposing bodies.)
Chiko's Extended mod has also been simmering for a good, long time, and is quite popular. He's a veritable whirlwind of activity, creating a prodigious amount of new items, moves, creatures, and other content. Most of his stuff is pretty well in the spirit of the game, too, though it sounds like there may be balance issues based on what you're saying. I think his approach is to throw things in there first, and tweak/cull them later. There are definitely a few silly things among the changes, but for many players, his mod fills several gaps in the vanilla game (e.g. moves, items, and recipes that many expect to be there but aren't).
I haven't had a lot of exposure to the other mods yet, so it's hard for me to comment. Looking at the list of current and WIP mods is pretty impressive, though. People have been busy!
Anyway, I just wanted to pop in and mention my take on the lore vs. mods stuff.
Oh! And re:
thesheeep 's question about Hidden Lake, no skills are required to complete the quest. If I had to guess, it may be the poor UI at fault. (a.k.a. me) When you receive an item in an encounter, it floats across the screen and you get an "Items" button below the "Confirm" button to indicate loot. It can sometimes be easy to miss, though, and I suspect that's what happened in your case.
Or, you know, it's a bug
In which case, my bad and let me know!