Ketsurui Military Sector
Himiko and Hanako's Star are both to my understanding still under Kuvexian occupation. Scrapyard System was recaptured in YE 43. No population data at all. However, my sense is that they are fairly populated.
Motoyoshi Colonial Sector
Asura, Hici'emi, Jiyuu, Kotoku, Lor, Nyli, Yuujou have population data.
Koukotsu included future population growth. With that included their population is 326,793,973.
Tange mentions that a planet has a few thousand people on it, but also mentions signifigant numbers of others.
Gensou, Mitsuya, Miyamae, Shugosha, Siren and do not have population data.
Fujiko Region
Demibear has provided population data for Fujiko, Rufusland, and Ukmirt.
Other
Ayano, Mwigflukbajik, Sharie, and Shurista have population data.
Ake, HX-2, Miu, Xyainbor, YC-04-Proclycon System does not have population data.
I think Miu is currently under occupation.
Saiki Cluster
Daichi and SX-07 have population data through a planet. SX-07 should probably be renamed to Minato.
SX-03, SX-05, SX-06 don't have population data.
Samurai Military Sector
Valentine does have population data.
Arzank, Jun, Virgina, and Veronica don't have population data.
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There are 24 places without population data. The list of places that don't have population data is Murf, Tsuyosa, Yicuqibu, Hanako's Star, Himiko, Scrapyard System, Gensou System, Mitsuya, Miyamae System, Shugosha System, Siren System, Tange System, Ake, HX-2, Miu, Xyainbor, YC-04-Proclycon System, SX-03, SX-05, SX-06, Arzank, Jun, Virginia, and Veronica.
There are some places where I can infer a rough guesses at population. (although if I'm guessing, I'm probably going high)
I don't know if I've missed any Yamataian systems. There are a few where I question if Yamatai claims them. Mwigflukbajik and some of the systems that seem to basicly only have been explored for example.
In terms of data collection, some systems aren't on the big automatic list for various reasons. The most common being that their Faction struct is set to a faction other than Yamatai. (ex Hidden Sun Clan).
On a random tangent, I think that Elysia and Abwehran need to be something other than empires. We may need a subfaction stuct as well becuase 87 is a very big long list, that said having them all in different factions is fine if we remember that when we pull the struct data.