I've seen this issue as well on an Enterprise level Cisco LAN with (4) ATV's. My hunch is that the 5.3 update has produced a "bug" around the ATV's ability through Bonjour to broadcast its presence on the LAN. It is almost like the broadcast goes to sleep (so to speak) at some point and this is why the ATV "disappears" from the Airplay list. As had been mentioned in previous posts, we are all finding ways to reawaken the broadcast only to find that the ATV "disappears" from the Airplay list.
My new Time Capsule is the latest 802.11ac and I still have the problem.
I restored my Apple TV today using iTunes but it has made no difference.
There does not seem to be any way of reverting back to the previous version of the software.
I have used the Apple Feedback pages http://www.apple.com/feedback/ to report the problem.
I hope everyone else does the same
I've discovered that if I disconnect the ethernet cable from the Apple TV and reconfigure it to use wifi then it all works as expected:- The Apple TV appears in the list of Airplay devices on my MacBook, iPhone and iPad without having to restart the Apple TV and it wakens up from sleep when selected. It also see my iTunes Library and Photos on my Macbook.
Whilst I would prefer to use ethernet rather than wifi I consider this a temporary solution and continue to hope that Apple will address the problem in a future release.