Is this duplicated with https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/spglib/default.nix or is this just the python variant?

It is the same package source but this derivation builds only the C-API/library of the package. The other derivation builds the python package.

Would it be smart to reuse the source from their to not potentially have different versions in nixpkgs?

I am not sure how that would look like, as they live in different package subspaces in nixpkgs. Having different versions may not be an issue as it is unlikely that one project depends on both C-API and Python at the same time.
This solution now is at least of low complexity.
Do have a suggestion or do you know of a similar case?

Do have a suggestion or do you know of a similar case?

The change would probably need to happen on the python side because it would be easier. There we could do something like in the python top level file:

spglib = callPackages ../.. {
  inherit (pkgs.spglib) src;
};

But I am not sure if this would be a good idea.

I took a look at the python package: it uses fetchpypi to get the sources and simply switching the sources to the plain GithHub sources failed and would require more work. I would suggest to keep the plain C-version and python version separate for now.