Do the zero pop colonies have facilities on them? They could be automated mining posts or listening posts or fuel depots. Or they could be remains of colonies that got bombed by someone else. The colony designation doesn't go away even if there is nothing on the rock.
as far as i can tell, none of the colonies have anything on them, except for two: the capital has 0.00142395685862664 population (i guess that's in millions?) with a colony cost of 1.0944, but no radiation or dust. the other one has a similar low number of pops and colony cost 2. the race also have commanders and some 55k academy crewmembers but I don't know where those are. their hoeworld ID is 0, like for the swarm.
they have very few log entries (45) and all of them seem to be just those commander bonus changes and retirements. first log is at 5671778350.0, last is 5827190355.0. current time is 5828371155.0, so their last log is not that old, they are still active.
two of their systems is also known for another race (who I am allied with), yet they haven't seem to had contact with any other race.
Weird.