We automatically package all extensions from https://extensions.gnome.org/ but the the official GNOME extensions packaged in gnome-shell-extensions package are bit of a special case since they are a part of a single project and are packaged together as such. We should either remove them from the list of automatically packaged extensions or make the attributes point to gnome.gnome-shell-extensions.
If you have both packages installed, there is probably a file conflict so Nix chooses the file it ¿sees first?
Since it is automatically packaged, it is indeed packaged incorrectly. The system is not smart enough and will require a human intervention. @piegames I wonder how hard it would be to scan extensions for typelib includes and resolve that automatically. Then again there are external dependencies on programs installed to PATH, which would be much harder to catch.
GNOME Shell extensions installed through Nix should work. If they do not please open a bug in Nixpkgs issue tracker.