The more information that nUI acts on the lower the fps. What I tend to do in raid situations when the fps can drop severely is switch to party view as being a healer I can use grid to heal people with.
Having say 25 unit frames to update with all the information that nUI calculates regularly is bound to impact the fps. That is one of the things that Scott is working to correct in version 6.
However, that said. I only had major fps problems when Wrath and 3.1 came out so they obviously changed things big time there to impact on your system anyway.
I even tried disabling nUI during a raid to diminish the fps problem. I couldn't even play the game as I had spent so long with nUI as my main interface that I just can't play without it
In Dalaran I usually sit at about 60fps dropping to about 40fps on busy days but in large active raids it can drop to 5fps or lower. Switching frame display helps alot but doesn't negate it completely. Also, extra graphics effects that aren't needed I have turned down in the past when I had a lower end graphics card that worked fine pre Wrath.