I strongly recommend ray trace objects ON, ray trace everything OFF.
Don't worry too much about whether ray tracing might help your clouds. Most of the existing advice and accumulated knowledge about cloud settings, detail levels etc. applies to the micropolygon render and I think you should continue rendering them as before. Only if you are rendering a scene where you can't see much terrain detail would I think about trying the ray trace everything option, and even then the quality-vs-speed tradoff probably won't be earth-shattering.
We are planning to provide options to render clouds and atmosphere using ray tracing without affecting terrain quality in future versions. Having the option to ray trace everything in current builds allows us to research the implications of doing so. Feel free to experiment, but I don't think it's the right setting to use for most scenes.
Regarding speed of ray tracing individual objects, there becomes a point where ray tracing the objects is slower. The big speed gains come with large, complex objects or populations.
Matt