Compare the difference in numbers flying and total versus the ENY and you will discover it is based on the Total numbers of a country.
It's logical. Numbers flying are often much closer than total numbers, hence the reason the OP posted this topic to begin with. Also, numbers flying vary much more quickly over a wider range than total numbers in the arena. Six or more people on the same side may all get shot down, auger, or end sortie at the same time versus the same number suddenly logging off.
Bad for business? Kicking people out of your place of business that have paid to be there just because they aren't doing anything while they are there. How could that be bad for business?
Just randomly disconnect people from the side with the numbers instead.

wrongway
Lets not get off on a tangent this would only affect someone who has left and is logged in for a extended period of time, this amount of time would be whatever that HTC would deem a appropriate, 1-hour two-hours whatever. I have logged in many mornings only to find people that were playing the knight before still logged in but have been away for many hours, I have done this myself

I'm not proud of this but I would have no issue with timing out and having to relog because of my extended absence.
The other approach would be to only count active people using the same criteria, if someone is in the tower and hasn't had any activity for a extended period of time, as far as I know if your logged into the game you are counted too your sides numbers flying or not.
The way I see this it would make the ENY value counter a more real time number, kind of a fine tuner.