By default iOS will backup all local disk containers to your iCloud account (or iTunes). Of course you can configure iOS to exclude the Disk Decipher app from the iCloud/iTunes backup, but that will exclude all local disk containers from the backup.
Version 2.5.2 of Disk Decipher adds to the option to selectively exclude a disk container from the iCloud/iTunes backup. To enable this option simply swipe a local disk container to the left and select Settings:
which will open the Settings view allowing you to exclude the selected container from the iCloud backup: