If it's any help, I also HAD the same problem and have now resolved it.
I have ATV 1 and Airport Extreme (old version) so don't have the latest features of a guest network and a private one however this sparked my interest.
My iMac uses WiFi to connect to the network - and so did my ATV originally. I plugged the network lead in recently when I noticed the ATV went missing from the DEVICES list in iTunes. I switched off the ATV and restarted (same with iTunes and restarting the iMac) to no avail. Then I remembered that there was also a firmward update a while back for the AirPort Extreme (which I dutifully installed). I removed the network lead, restarted ATV and iTunes and hey presto! My ATV appeared in DEVICES in iTunes.
I can't help but think that the latest Airport Extreme firmware update (for older models - pre Time Capsule) is somehow keeping my wired and wireless network seperate. As soon as I plug in the cable again, it's gone from devices. Remove the cable and connect via WiFi - It's back.
Maybe a new firmware update for Airport is needed?
Hope this helps!