Military bases, missile silos (which is why there are a shit ton of dots in states like Missouri and the Dakotas), airports, steel mills, chemical plants and it looks like even vehicle assembly plants.

I'm in Ohio and I can tell that one of those dots is directly on top of the huge General Motors assembly facility in Lordstown (which recently closed). I guess anything that could be repurposed to build and support war machines was considered as a potential target.

towns over a certain size will get nuked

I mean yeah, that's the point of nuclear warfare. Kill everyone so your enemy can never justify saying "Well it's not going to be that bad".

It seems to be exactly that. I don't know what Santa Fe's population was in 1990 but my hunch is was just over 50,000. When I checked the New Mexico map - sure enough Santa Fe is a target.

Santa Fe was (and still is) a tourist town. As far as I know - it has zero military or strategic value. The only thing that existed (and exists) here in vast amounts is very bad western art.