Ubuntu has traditionally had some default folders. Most of them (e.g. Music, Videos) were there because they were intended to house a specific type of file. Desktop, however, was there because it was special in that its contents would be shown on the user's desktop.
This doesn't seem to be the case anymore, since Unity's desktop only shows the wallpaper. How is this going to be handled? Will the desktop folder be assigned a different purpose? Will it just be removed from default installs? Will its contents still have a special place? Also, can we expect Unity's desktop to show anything else besides the wallpaper in the future?
Desktop unity in 11.04 (natty) will have the standard nautilus based desktop activated again, so you'll be able to put icons and launchers on the desktop for 11.04.
For 11.10 we are completely rethinking how files are managed and accessed so it is likely that this question will become moot in a years time.
The desktop folder is unused by Unity, other than acting like a normal folder. It is still used by other desktops environments such as GNOME/Ubuntu.