After 3 years and 2 months… I received a lot of points because of this question here on stackoverflow.
So yesterday I decided to revisit this topic :).
Using fcntl and F_LOG2PHYS is possible to check if files are using same physical blocks or not.
So I made an utility using this idea and put it on github (https://github.com/dyorgio/apfs-clone-checker).
It is only the first release guys, but I hope that the community can improve it.
Now maybe a good tool to remove duplicated files using clone APFS feature can be born. >:)