In most games I don't play mods. Since usually, if it's a good game, the base game satisfies me, and if it's not a good game, I'm not going to bother with mods.
However, Civ is somewhat different since it's a historical game, and thus lends itself naturally to historical mods. Most of my Civ4 time lately is in mods. Civ3 is usually the base game, but not always. I haven't played enough Civ5 to be ready for mods of it (unless there's a more-than-one-unit-per-tile mod with good AI, in which case, I'll skip right to mods).
The mention of instability/crashes is interesting. This seems to be much more of an issue in Civ4 than in Civ3. I think it's because Civ4 allows more elaborate modding, and thus more ways to screw up. Civ3 does have a few gotchas, but they're usually caught before the mod is released. But how common bugs and crashes are also depends on the mod. Some teams and modders are very good at making sure their mods are stable; others aren't (this mostly applies to Civ4; again, this isn't really much of an issue with Civ3). However, I've never seen anything nefarious in mods, and have never had anything worse than a crash to desktop happen, so I'm willing to try out mods. I haven't tried Civ5 mods, so I'm not sure where they stand on the stability/crash-less-ness spectrum.
I didn't vote since I'm not the target demographics, mostly playing III and IV and being someone who does play mods at least sometimes.
It seems low as a percentage.
Consider this baseline -- all people who have purchased the game thru steam would be 100%. All people who have started up the game would be probably in the 78% range (since that's the amount who have an Ancient Ruin achievement, and that's probably the single best indicator of "have you at least TRIED the game?") Of the people who loaded the game, only 40% of those have dropped a nuke on someone else. It either means that only 1 in 3 people who purchased the game finished A game (since even if you were just playing one, wouldn't you drop a nuke just to try it?) or that achievements really aren't that big of a deal to the general populace. If people were REALLY worried about achievements, they would do something so simple as that to get one. That seems to me that the majority of people aren't. Achievements cater to this very small subset of people who don't consider a game "Complete" unless they obtain all of them. I personally find them contrived and a nonsensical way to introduce replay value into a game at no cost to the developers.
I don't know, in all the time I've played Civ3, which is over 10 years now, I've probably only used nukes on a single-digit number of occasions. There's a variety of reasons to not use nukes - mutually assured destruction, not believing in nukes and thus not wanting to in-game, usually having games finish before nukes come around. And that's not even counting those who play the game for half an hour, do something else, and it sites in their backlog for years. So 32% does not seem low to me.
But I also think most people don't really care about achievements, or at least not so much as to go out of their way for them. Look at most any game with them, and there's almost always several with something like 0.2% accomplished. I don't think they're totally useless - well-implemented, they can be a decent source of ideas for gameplay variants, although the grindy ones are probably more common - but I don't think many people are completionists with them. So I agree with your conclusion about achievements, even if the percentage doesn't seem low to me.