Well, not that it appears anyone is actually reading this entire forum, but I'm posting an update anyways. It's actually not as straightforward as I originally thought. Since I had just correctly received achievements for finding anti-matter speck and face of gozu, i thought all new achievements were working properly, however, this doesn't appear to be the case. I just hit 100 merchants rescued, but did not receive an achievement, so it appears that the variables for achievements based on completing a task X number of times were not being tracked properly.
It's possible that the number just wasn't being counted earlier, but now is, but I am skeptical of that interpretation, as other achievements appear permanently borked, such as fighters and capital ships killed, so I suspect somehow the variables in my game are no longer corresponding to the ones that GOG is monitoring at all.
I normally don't really pay attention to these achievements anyways but since I was enjoying this game and had gotten a bunch of achievements initially without really intending to I got a little bit interested in completing the remaining ones, so it's frustrating not to be able to. I'm halfway tempted to just start a new game to see if those stats would be tracked correctly then, but I'm also worried they still wouldn't update properly, especially if the achievements are based across multiple characters.
All in all, makes me slightly wish I'd just gotten it on steam. Oh well. Anyways, buyer beware. This is a good game, but GOG achievements are hit or miss, so if that matters to you, maybe buy it on steam instead.