Will the new Unity desktop be programmed in Qt?

Unity is built using some GNOME technologies like GTK and gmenu, and some other technologies that are not officially part of GNOME, such as Compiz, Zeitgeist, Software Center, and other bits from the Ayatana project.

However for people who use older hardware or have driver problems the Unity 2D interface will be available in 11.04 and is programmed in Qt.

I would suggest you also read up on the future of GTK+ 3.x, Clutter, and related technologies. Using Qt as the basis of the Ubuntu desktop will not automatically make the desktop any easier to use, any "prettier", any "cooler" or any more stable. Furthermore, it would be more useful to forge ahead on a path of greater cross-toolkit standards (ref: freedesktop.org) and greater interoperability, not on consolidating everything into Qt.

At UDS Mark Shuttleworth mentioned, that one of the things that must be done until Unity will be ready to use, is to make it compatible with qt, so that these two could cooperate.