seat stays have a direct effect on rear end rigidity, so stays of differing lengths, no matter how aesthetically pleasing (or otherwise), are going to affect bike handling, particularly under acceleration, i would have thought. maybe not though - i don't know.

either way if i was contemplating buying a bike with assymetric stays i would need to know that a team of rocket scientists had spent three years and $43456789076434567887543.65 on figuring out why it was that way.