The heroes deal with the far frontier, so they tend to encounter only very small colonies - typically, village-sized communities based on sustenance farming. When Sisko bombed a "Maquis world", his nemesis Eddington believed that "hundreds of thousands" would be displaced if Sisko continued his actions on other planets
. The single world thus only had tens of thousands at most...
Basically, the only witnessed colony that appears to have been founded by more than just one shipment of daring frontiersmen is Deneva from TOS, an old freight hub past its prime. In "Operation: Annihilate!", the world had at least one large city with high-rise buildings, but interacted only minimally with the rest of the Federation (it going silent didn't raise eyebrows for a full year
!), and only had "almost a million" people, of whom "more than 100,000" lived in the city we saw.