Personally, I'd be of the mind to incorporate any populations moons might be capable of supporting into the max population calculation of the system normally and without a special structure, just to simplify it. But then, that removes anything "special" that a moon around a planet could provide. I also agree that such a habitat structure would, realistically, be capable of it's own energy generation. Too many things could go wrong with a facility in a vacuum; the last thing you need is someone accidentally (or purposefully) cutting a power cable which causes all of the moon colonies in the entire system to suddenly be inhospitable.
Like I said, the structure has a clunky feel to it. One successful sabotage could take out a bunch of energy reactors, preventing people on the moon from breathing. One successful sabotage could possibly take out this single "moon colony structure thingie", which would
kill every person living on any moon throughout the affected system (seems silly, right?) And lastly, 200 energy is a pretty huge drain, which makes it likely that the structure would be disabled in an energy-type crisis, which will also kill off the population living there (which any self-respecting democracy would be unable to do in good conscience.)
(I'm going to make the assumption that the "moon colonies" would be the last place population grows into and would be the first place population is subtracted from during starvation/bombardment/etc.)
I think just terraforming the moons makes things smoother from a gameplay perspective. And while terraforming the moon might sound improbable, it seems that someone has at least
thought about it. Besides, we're terraforming Pluto in the game, and it has
2% of the mass of the Moon.