It is not possible for current TUS to accept more than 2 communities. However it is fixed in TUS2 (It is already coded on my hard drive :p), even though it is possible to have infinite communities there, again system limits you to 2, but there will be ways to push your limit from 2 to any number.
On the subject, TUS keep tracks of communities, mark their activity in various parts etc. The more communities you have, the more stats will be created, which is no problem for TUS, but that's at least a reason not to clog the system.