nUI has to be coded specifically to look for certain bar addons and shift the top bars down accordingly.
This is either done within nUI itself or as a plugin.
The following I believe are built into nUI
Titan Panel
Bazooka
ChocolateBar
Fubar
The respective files that make the changes are inside the integration folder.
And these are plugins for the respective bar addons:
http://www.wowinterface.com/download...injaPanel.html
http://www.wowinterface.com/download...onBazooka.html