I will be deploying Backup Exec 2010 R3 to an environment with multiple Windows Server 2008 R2 Domain Controllers.
Do I need to backup Active Directory off of each DC? If yes, would I need a BE Active Directory Agent license for each DC?
If you backup the Shadow Copy Components on each DC (and you should) then you're backing up AD. You only need to purchase the AD agent if you want to do a granular restore of AD objects.
Because Active Directory Sync's off of the "Primary" or Main Server IMHO There is no need to backup the AD from the other AD Servers.
So, No, an agent for that on the other Server is not needed.
You will still need an agent to back up their files though and obviously other Services if they have any like SQL.