There’s little doubt that global warming will affect clouds, but since it’s very hard to measure the effects, it’s not clear if clouds reduce or increase the warming caused by carbon dioxide.
“Clouds have long been acknowledged to be the most unpredictable important part of the climate system,” said Matthew Huber, a climate scientist at Purdue University.
Some evidence suggests that the climate models used to project how human-caused climate change have underestimated climate feedback effects that can either enhance or weaken the warming caused by greenhouse gases. As a result, “there is a tendency to think that shiny, white, reflective clouds that cool the planet might diminish in a warmer world, or that the high, thin, heat-trapping clouds might be enhanced instead. But, the jury is still out,” Huber said.
This NASA video animation includes a good explanation of the role of clouds in the climate system, and the 2013 global climate assessment from the Intergovernmental Panel on Climate Change includes a detailed chapter on clouds.