Without additional lore, we can only speculate.
Some people, such as me, do not that that "population" is actually a measure of the planet's occupants, but rather a measure of its citizens. That is to say, population increase represents bringing surface settlements and people under your control.
The biggest problem I have with the literal interpretation of population as a head-count is that this game has a time-scale of, at most, a handful of years. It's certainly not long enough for multiple generations to pass and therefor the adult population shouldn't actually be increasing much at all. Even presuming the more ridiculous logarithmic scale, there's no way that the population growth makes any sense in this context. You can counter with the theory of immigrants, but this raises the very valid question of why people would immigrate into a warzone, or a world enslaved by the Vasari, for that matter. There are also other valid questions; where does population go when a planet "turns neutral" due to culture? Who builds and maintains the planetary militia? Who are the Vasari "enslaving" if the planet was unoccupied before their arrival?
I feel the most reasonable interpretation of the colonization process is as follows:
All planets are initially occupied by people (most, if not entirely, human in origin) who have small standing militias to protect them. These people are less technologically sophisticated than the "core worlds" from where the TEC originate, limiting their ability to defend themselves. When your colony vessel arrives, a small military occupation force is sent to the surface. This occupation is initially expensive to maintain, but with investment you can build an industrial complex on the surface of the planet. This would explain underdevelopment tax quite nicely, and the "cities" and "traffic" we see on larger planets would be advanced distribution centers built by the new management. Orbital bombardment would then not necessarily be indiscriminate killing, but rather a directed assault on the surface-based military installations. This would also explain militia "bombarding" their own planet; they're attacking enemy invaders who reached the surface.