Should I use Multiple or a Single SQL Database?
This greatly depends on your particular Network environment.
If you have permissions based on NDS OU's that are based on Cities, and Data is only contained within these OU's and the Data permissions is limited to the city OU, then you could use separate SQL Databases for each city. But if you have permissions spread throughout the Data directory structure that cross OU boundaries, it is recommended to use a single SQL Database so that there is no loss of permissions on any resource because a Mapping entry was not found within the Database to properly translate to permissions from NDS Objects to AD Objects. If no entry is found within the Database, the permissions will not be applied.
Even if you are using one database, Multiple NDS Migrator consoles may be needed depending on the functions/speeds between sites.