I'm now almost completely convinced it is a software issue. I mostly only get it when a particular sound is about to be played, usually the Siri beeps, email notifications or the dictation button on the keyboard. I am dictating this sentence right now and it just popped as the beep played.
There have been a few times where the pop has been quite loud, more like a loud snap that seems like it was played at full volume. However, it's always when I am using the iPad Air 2, never when it is not in use/on standby.
This is quite sad to say but I haven't exchanged my unit since I'm getting used to the pops. I know it isn't something I should have to live with but as I got it on release day, I am outside the 14 day money back guarantee or exchange policy and anyway… People's replacements seem to be the same which is another indication to me that it is software related.