Running at native resolution gets the most out of your system so given two monitors the same size but different native resolutions I would expect higher frame rates on the monitor running at native resolution rather than windowed.
In extended mode, the monitors don't have to be run at the same resolution. You can run each monitor at their native resolution.
Running at something other than native resolution: I don't know if there are performance effects, but there are definitely visual effects - similar to what happens when you rescale an image. This link gives a good overview (at least, better than I can explain) of why this is: http://www.cambridgeincolour.com/tutorials/image-interpolation.htm
Curtis