It is interesting to see if they do it, although I doubt till Sins 2.
If they have no game play-related or strategic purpose then while they might make for nice eye candy, they'll probably just increase the amount of in-game lag.
Well, you can say the asteroids that currently orbit each planet now can also be called moons, so replace each moon with a moon type, each with a bonus of sorts.
The problems with moons is that the develops will have to drastically overhaul the path finding. As it is, ships don't move smoothly, moons just adds to the problem.