NGUI doesn't really handle it. The UIRoot's height changes if its pixel perfect, so it statys the same size on the screen.
If you have the height to fixedSize, then stuff is resized to be the same size to the relative height - it will "fit" the old height into the new height, so if it changes from 960 to 640, everything will be smaller by the same factor.
Either way, it's a good idea to manually handle it yourself.