Would be cool, but I think it would be better to have in a seperate simulation. If the program would have to simulate atmospheres, it would just take CPU from the normal simulation (except if you have multiple cores and it is implemented to utilize different cores). I think it should be a simple animation by default, or a very simple simulation, maybe only simulated on planets taking up more than x% of your view (which could probably be approximately calculated from your view's distance to the planet, its radius and maybe FOV).
But it would be cool, and I wouldn't have a problem with it either as long as you can choose not to simulate it.
But if it IS added, then I also demand the ponies implemented so I can watch Rainbow Dash floating on simulated clouds on a planet with rainbow rings