How are your backups currently stored, simple copies of the files like you would make with rsync? I assume your on a Linux NAS, in which case fdupes would likely fit the bill. meld would be another option, and it also has a GUI if your NAS isn't headless.

For future backups restic might be a nice option as it deduplicates itself each time you run the backup. You can set retention policies (i.e. 7 daily, 4 weekly, 2 monthly, etc...) that only keep regulated intervals of backups.

The only thing I can think of is to do a restore of all the backups in sequence, assuming they're all of the same thing. That would give you one consolidated image. Then you could run some deduplication and take a new single backup, if desired.

But really it's so subjective that I don't think there's really any way to automate it. I would mount all the backups, go through everything, pick out what you want to keep, and delete the rest.

Look at it this way. If you've had the backup for years, and never needed to restore any of those files, how likely are you ever need them in the future? Even if you did delete something you later wanted, how life-threatening would it be to not have it?

Or you could take the easy way out and just add more storage.