Just in case it's still useful, the main thing that affects grain in clouds is the quality/samples setting. Same for the atmosphere. Sometimes it's difficult to determine if noise is coming from clouds or atmosphere though, so you should do crop renders with different settings to test in these cases.
Also enabling raytraced shadows in clouds or atmosphere will not help with grain in any way, and we generally recommend you do not use these settings unless you have a very specific reason and need to do so. The most common need for it in the atmosphere is if you have a problem with the sun glow being visible through terrain when the sun is low on the horizon. Raytraced shadow settings in clouds and atmosphere basically enable shadows from terrain either into the atmosphere, or onto clouds, respectively. In most cases neither is present in a scene. Enabling them just makes render times a lot longer.
- Oshyan
