There's nothing in the AirPlay protocol that prevents it from working at higher sample rates or bit depths, but the current generation of AirPlay devices seems to be limited to streaming at 44/16 resolution. This is true even of Apple TV which, despite having a 48/16 optical output, also streams at 44/16 when used with iTunes, iPod, etc. This means that any 48/16 or higher content you may have will first be downsampled to 44/16 by iTunes, etc. for streaming before being upsampled again to 48/16 by ATV, losing quality in the process. (AirPort Express simply output the 44/16 without any further conversion.)
Having experimented with the Audio MIDI Setup app, I can confirm that this makes no difference to AirPlay streaming via AE or ATV, so I guess we're stuck with 44/16 for the time being. What would happen if some third-party software tried to stream at a higher sample rate or bit depth is anybody's guess – for example, the device might simply reject the stream – but given that AirPlay is a proprietary protocol, I can't see this happening any time soon.
What's slightly frustrating thing about all this is that a lot of these restrictions could probably be lifted via software updates to iTunes and AE/ATV as the hardware appears capable of supporting higher bit rates (e.g. multi-channel surround sound via Apple TV). However, since high resolution audio is not a priority for Apple, they appear to have restricted AirPlay devices to work with CD/iTunes formats only, which use a 44/16 audio resolution.
If people would like to improvements in this area, a good place to start would be reporting the issue to Apple via the following forms:
http://www.apple.com/feedback/appletv.html
http://www.apple.com/feedback/airportexpress.html
The more people that do this, the more chance there is of this happening! Personally, I'd love to be able to stream high definition and/or multi-channel audio to my amplifier via AirPlay, and this would certainly buy Apple a good following in the audiophile market… Apple TV 3, anyone? 😉