The current plan is to include 90 apartments available in each complex, but this number can be raised as needed for each ward, so don’t worry about room availability.
So it looks like 90 is just the minimum, and when needed will be increased. Its less that Balmung (and other large servers) will be out of room and more how long it will take them to add in more rooms.

http://forum.square-enix.com/ffxiv/t...51#post3853951