Airport Express is limited to 44.1 kHz as you probably know regardless of source material.
AppleTV2 annoyingly upsamples output to 48 kHz.
If you used an Express you couldn't play to it from AppleTV2 (only AppleTV1 did that), you would have to play from iTunes or iTunes using Remote app on iPod Touch/iPhone.
The 48kHz out should be user selectable as I can't see it doing any good.
Send feedback:
http://www.apple.com/feedback/appletv.html
Also suggest it might be nice to allow passthrough of 16/24 bit 96/192 kHz files and other common variants if the files are present as such in iTunes.
AC