I've run with clouds (in the new cloud system) in about 20 special event runnings. Out of the 500 or so players in them, I got 3-5 who said that they had significant frame-rate problems. So, for whatever mix of clouds I was running, it didn't seem to significantly impact the vast majority of players.
The new clouds system has about a dozen different cloud types, so it is possible that particular types or particular mixes cause issues, but other types or other mixes do not.
I'm running "This Day in WWII: Battle of Britain" tomorrow (runs at 3 pm Eastern and 8:30 pm Eastern in Special Events II in case anyone wants to give this fun event a shot). I'll try out clouds there and see how it goes to see if the design I have in mind will work well for the upcoming Battle of Britain scenario (running 4 Saturdays in September, starting Sept 7, running at 3 pm Eastern).