Kaigoss, spot on. Although I believe that the ATV3 does do true 16/44.1 output but dont quote me on that.
This is the problem with apple, they flower up the good bits but don't release good hard facts about their products. Yet... I still buy them.
Am I right in assuming you already have the AE, judging from OP. i would just give it a go. I know that Soundman did an optical out mod using a camera kit or something on an ipad thru a bit one and the sound was twice as good thru the optical and DAC(i think).
I'll dig out the link so you can see it for yourself.
EDIT: Here is the link for video
Actually yep just to confirm ATV 2 and 3 resamples all sound to 48khz/16bit, so CD quality will sound pretty good but any HD audios you have probably not so.