AFAIK, Atom is a chip with hardcoded power-saving features (and a lot of enhancements left out to make it run cooler), a low MHz count and a small cache.
Depending on the chosen OS, the presence of upgraded hardware or not (e.q. HD replaced with a faster model), it will make WinUAE run smoothly or not.
Intel went real cheap on that one, but again you might get lucky if you try hard enough. This said, cats don't make dogs. (I'd rather go with AMD Neo -K8 powaaa
, personally)
I use a Yahoo Widget to monitor CPU usage : SystemDashboard. May be some other processes steal your CPU cycles while WinUAE is at work...