The way that the new clouds are implemented, seems to be very hardware dependant as far as performance goes. I've heard stories from both sides, where the only real difference between machines was the brand of GFX chip being used on their video card. I use nVidia and only see a slight hit to the frames, while someone using another brand gets a slideshow.
Performance issues might also be connected to the number of clouds, and how much overlap there is among them. Fewer clouds in strategic places of differing sizes, spacing and altitudes might be a good compromise between having a flat cloudless sky and having more of that "flying" feeling that the majority of players can tolerate.