I've been a sysadmin managing SunOS and Linux systems at scale.
I've had personal machines running a variety of OSs: FreeBSD, Linux, Windows, Mac OS, OS X, to say nothing off all the different filesystems involved across those OSes.
In all that time, I can't think of a single time I've ever bothered to de-duplicate files.
Once upon a time, you used to occasionally need to defragment some file systems. But it's been more than two decades since I've even thought about defragmenting. Every modern filesystem just handles that automatically.
What even is the use case where folks end up with enough duplicate files that it's worth worrying about?