nextcloud-client ships an extension for nautilus-python so you will need to install that system-wide:
environment.systemPackages = [
pkgs.gnome.nautilus-python
];
That sounds like this upstream issue: [Bug]: Nautilus integration: Nextcloud shares shown twice · Issue #6218 · nextcloud/desktop · GitHub
The fix will be part of the upcoming Nextcloud 3.12 release.
You may want to open an issue in Nixpkgs, asking the maintainers of the nextcloud-client package to backport it. Or even better, open a pull request.
This is not supported by GNOME Shell. One of the GNOME Shell developers created a merge request with a prototype but that has been stuck on lack of design.
If the Nextcloud provides AppIndicator API, you might be able to achieve it by installing gnomeExtensions.appindicator, re-logging into GNOME Shell, and enabling the extension in the Extensions app.