Btrfs Backup – Ideal Storage Scheme with External USB HDD

You can use the bedup utility to de-duplicate the identical files. Once you've installed it, usage is fairly simple:

# bedup dedup /path/to/btrfs

You may need to set your snapshots writable (btrfs property set -ts /path/to/snapshot ro false) so it can de-duplicate them. You can change them back afterwards.

Note that depending on how many files you have, it could take a while (it first looks for files of the same size, then compares those files... so if you have a bunch of large files of the same size, that can take a bit.)

Finally, you can run it again from time to time and the future runs will be much quicker as it keeps track of the btrfs generation and uses that to skip old files.

I will just provide a short answer because I think this is being overthought.

If you read the main kernel wiki about the btrfs (sub-)commands, you will find that there are two commands for:

1. making a "backup": btrfs-send
2. and restore: btrfs-restore

Just in case, this means that it is not (designed to be) a backup, but to be an snapshot filesystem, with the idea of rolling back if needed, not as a backup but as "flexible".

Therefore — no, do not use it as backup — use it as a versioned filesystem where you can test things and go back. Don't rely on it.