Suggestions - Enabling EFS on FileStream Data for SQL Server
I can't speak to whether or not EFS should be applied per folder.  However, there is a security consideration that seems to be worth an answer here.  

Check out this post from David Browne on the MSDN forums question Can FILESTREAM directory containers be encrypted with EFS?:


  Note that during a SQL Server backup of FILESTREAM data, the data is stored decrypted. A restore operation to a normal volume therefore will result in decrypted values.


So if you are using native SQL Server backups, you will need to keep this caveat in mind from a security / compliance standpoint.