I think I'd prefer to backup the dehydrated data. HOWTO21767 Best Practices for Backup Exec 2010 Deduplication Option Gives some advice in this regard:
Perform regular backups of the deduplication storage folder and the database folder to removable media. In the backup selection list, the Backup Exec Deduplication Storage node is located under the User Data node under Shadow Copy Components.
Remove the Backup Exec Deduplication Storage node from the selection list when you create an Intelligent Disaster Recovery job. By removing the Backup Exec Deduplication Storage node, the deduplication storage folder will not be restored with Shadow Copy Components, but it can be restored from the separate backup if required.
What should the backup jobs look like for backing up the deduplication folder? Can I configure an incremental backup for the Deduplication Storage Node?