In Gnome 3, will nautilus still be used to handle the desktop, or will it be some component of Gnome Shell or something? If one decides to not use Gnome Shell, how will the desktop be displayed?
The Desktop is still handled by Nautilus. In Ubuntu 11.10, the Desktop icons are still displayed by default. If you install and log into GNOME-Shell, you will have a blank Desktop by default (only while in GNOME Shell).
From what I understand Ubuntu 11.10 desktop management is handled by Unity, that's the interface. If one were to decide not to use Unity there is a Unity 2D version, similar to the fallback mode in Gnome 3/Fedora.