Should you encrypt the system databases?
The answer is "NO".  

When you attempt encrypt a system database, SQL Server complains: 


  Cannot encrypt a system database.  Database encryption operations
  cannot be performed for 'master', 'model', 'tempdb', 'msdb' or
  'resource' databases.


However, it's important to realize that any successful encryption of a non-system database will cause TempDB to be encrypted automatically, to protect temporary objects. In fact, even if TDE is later removed from the user database, TempDB will remain encrypted.