Indy planets will produce colonists at the same rate as any player owned planet. The difference is that Indy planets CAN upgrade their own sector defenses and planet levels based upon the money they are producing. Say you have two Indy planets where one has 10% of the population creating credits and the other has 60% creating credits The planet with 60% of the population creating credits will grow alot faster in size than the 10% planet because there are more credits for it to work with.

Also, just because a planet has the money doesn't mean it will upgrade itself. It is random as to whether or not the planet will upgrade, what it will upgrade and how much it will upgrade what it has selected.