Ah, number of rows I was referring to is entire window, not the map. The minimum map size is 50x50. The reason it decided to give you 80 on first startup was because before that point the DPI setting hadn't been manually changed, and that will cause it to be confused at the actual size of the window being created according to Windows. In this situation, I believe the best approach is to just delete the whole cfg file and restart after changing that setting, in which it should be detected and set correctly. But you've already manually set it yourself so it's the same effect.
And no you're not making it less playable at all! Cogmind was explicitly designed to work with a 50x50 map, so you're set up just fine now. I was just referring to what was an occasional call early on in development for a viewable map area even smaller than 50x50, so that even larger fonts could be used. Playing with a map larger than 50x50, on the other hand, works just fine.