Look for grey speckled ground. It will be in some of the biomes that have scattered mountains and trees.
I see it, but there is no way to interact with it to create limestone mines. Possibly a bug?
Possibly. Is your settlement in the same region, with another structure adjacent to it? If the hex isn't highlighted it could be in a neighboring region, which you can settle to build the mines.
I dunno, I settled pretty close to it.