Hi Giulio,
For deduplication you probably need to install the PGP client in the machine where the backup agent works. What you are looking for is to access clear text files. It means that the backup process must be able to reach the files after the NetShare contents were unlocked, which implies access to the private portion of the PGP key to decrypt the contents. For an automated solution perhaps PGP Command Line would be the best approach to decrypt the files in bulk to allow the deduplication process to work.
If your backup software manipulates encrypted files, it will render them useless. It will result in garbled content.
PGP NetShare File Protection FAQ - TECH148964
PGP NetShare Basics FAQ - TECH148972
Symantec File Share Encryption (previously PGP NetShare) Compatibility FAQ - TECH148974
Probably the safest could be to copy the encrypted files "as is" and ensure the keypairs/ADK are available in case the business requires access to that data.
Usual recommendation: test the backups and test the ADK.
HTH
Edit:
Removed a misleading sentence:
The whitelisting/blacklisting is for data originated from a certain application. That is not the case of the dataset you want to backup.
Reference: Backup File Share Encrypted Files (Previously PGP NetShare) - TECH149223