Hello,
We CAN backup up MSDE 2000 through Backup Exec 12.0
Check Page # 18 of the Backup Exec 12.0 SCL:
http://seer.entsupport.symantec.com/docs/295304.htm
MSDE 2.x (SQL 2000 desktop) SP3A x86-32bit
MSDE 2.x (SQL 2000 desktop) SP4 x86-32bit
hope this helps......