My opinion:

For personal homes - Apartments will be sold within the villages, maybe like GTA housing but inside the house you can decorate and place furniture where you want. (rather than having the same place as everyone else)
If you're part of a clan and it has purchased some land within the village you can have a home inside it's walls (Like the Uchiha estate)

Clan HQ - A building for meetings and clan gatherings, however, will be unique. This could be purchasable in game via auction or by being sold by the Kage of the village. Once sold these clan HQ buildings won't be owned by anyone else and are unique to your clan. This prevents gatherings around 1 or 2 houses that are shared amongst many clans and also gives the game more realism.

Organisation hideouts - I was thinking these places can be places that are hidden around the map and taken upon by clans. There will be no officiality of it or anything but it will rather be like with Minecraft faction servers where people find a cave or something to make as their base. (I know some people in Minecraft created buildings instead of going into caves but this is just an example of my idea) This way if the Org hideout is discovered by Shinobi the Org can choose to relocate with ease instead of wasting so much money on a hideout that is purchased. Otherwise everyone will soon have word that a certain org lives in that spot and it will be targetted. No one said a rouge life was easy after all, you must be willing to relocate if you are to be discovered.

That is my opinion on the whole concept of living in SLO anyway