Add the following line to ~/.local/share/applications/mimeapps.list:
x-scheme-handler/nautilus=nautilus-handler.desktop
Place nautilus-handler.desktop into ~/.local/share/applications.
Place nautilus-hander into a PATH directory. I use ~/bin. Make this executable (chmod +x nautilus-handler).
Now nautilus uri scheme (example: nautilus:/some/path) links should work.