Enabling dedupe will only have an effect on active data, not those blocks that are protected by Snapshots. What I tell customers with large data sets changing is to minimize the Snapshot frequency when possible. Then figure out how long a dedupe run takes. Schedule the Dedupe run to run AND finish before the scheduled snapshot time. This will provide the best results. If the dedupe run take around 2 hours and if you take Snaps at 0800,1200 & 1600, maybe have the dedupe run at 0500, 0900 and 1300. That would capture most changes and be best in the Snapshots.
Autodelete may not be the best in this case. Most protections apps (like CommVault) take a snapshot and expect it to be there until it deletes it. If the autodelete removes a CV snapshot, it may get confused.
I am not familiar enough with CommVault to answer further.
Hope this helps at least a little.