EDIT After doing some more digging I found that you can launch nautilus as root and get access to the special URIs by using dbus. The command would be
sudo dbus-launch nautilus
And then the URIs are all available. To be honest I am not 100% why this works but some of the original information I found below may still be helpful.
The reason those URIs exist is because Nautilus uses a virtual file system called Gnome Virtual File System (gvfs) which is built on top of another virtual file system called FUSE. Specifically those URIs are configured in the
/usr/lib/gvfs/ directory named gvfsd-*. These are binary files so don't try and edit them.
When you mount a Samba share using Nautilus it uses the gvfsd-mount command (stored in
/usr/bin) to mount the share you specify. The share is then mounted in
/run/user/<UID>/gvfs/ where is your user id (typically 1000 for single user systems).
As for root being able to use these URIs, Ubuntu, and I'm assuming other distributions, configures fuse so that root cannot use the virtual file system for security reasons. You'll notice in the
/run/user folder there is no 0 directory for the root user. The
/etc/fuse.conf file by default is not configured to allow the root user access. This means that if your user mounts a share even the root user cannot view the share without configuring Fuse to allow it.
I have not actually tested giving root access to the Fuse file system or special URIs but you may have luck configuring it as described in this link or reading through the Fuse man page.
Sorry for the RTFM answer, but I couldn't find a definitive solution and it depends on what version of Ubuntu you are on as some of the directories/commands changed in recent versions.