Audio beacons aren't plausible to me as a mobile app developer. Mobile OSes have been tightening their privacy controls for quite some time. At this point you can't run an Android app in the background without the user knowing. You have to explicitly request access to the microphone. In recent Android and iOS versions, the user will be notified about which apps used the microphone when. Besides, constantly recording and analyzing an audio stream would have a noticeable effect on battery life.
How about apps that already have permission, like Shazam, Siri, and GA?
As for battery, they would only need to sample a second every few minutes, to see if there was a beacon afoot, quick DFFT, and they wouldn't need to analyze much.
Not saying it's happening, just that it's easily possible. Look how many apps have location permissions that don't need it.
