A package is non-unique if it is available in at least 2 repositories. Guess what. Repology tracks Guix as well which means many packages will be just in those two repos, marking them as non-unique.
If you want a non-misleading comparison you have to remove all these packages, which are actually managed by a different package manager every. from nixpkgs and put that into repology.
You can remove the entirety of the guix package set (26468) from the non-unique part of nixpkgs (71875) and it would still be the largest non-unique package set (second largest non-unique is AUR at 37900).
If you want a non-misleading comparison you have to remove all these packages, which are actually managed by a different package manager every. from nixpkgs and put that into repology.