Well, most people seem to run from a single folder using virtual config or one for the master and one for all the slaves with junctions or symlinks. I don't see many people using individual folders.

I'm not the technical guru that a lot of other people here are, but I would guess that the performance {and ease of use} gain from using fewer folders {all data being pulled from one location instead of pulling the very same data from 5 different locations all at once} is the bigger gain. AFAIK, and I'm sure someone will correct me if I'm wrong, addon writes are only done during logout, which is why if you force the game to shutdown instead of doing a proper logout, changes don't save. At any rate, the performance lost, if any doesn't seem to be a big enough deal to cause most people to want to spend disk space on multiple installs.