As of v9.0, BackupExec used "Active FIle Exclusion" to bypass Exchange, Notes, MSSQL and Sharepoint files during the flat file portion of the backup, in order to get rid of the "in use - skipped" messages without any mention of this in the job log
To backup MSSQL databases you need the SQL Agent and to include the databases in the backup selections
If you were not doing database backups, you are indeed well and truely SOL