I too have this same question - why doesn't ATV3 enable music to be played to multiple speakers from the ATV? I've had an ATV1 for several years, and ATV1 supports playing music to multiple speakers from the ATV. I'm baffled why the "new & improved" ATV3 doesn't offer the same functionality. I just bought an ATV3 but haven't fully retired my ATV1 for the time being, as this is deal-breaker functionality for me.
I beleive multi speaker output is strictly a function of iTunes. ATV1 was the hobby or beta environment and was a mix of OSX 10.4 (iTunes) and their developement of iOS. The multi speaker out was not a part of the further or current developement of iOS.
Still have an original atv out in the studio serving up music to the rest of the house... including the new appleTV2 in the living room