Just an update on this ARN-ATH flight:
So I refused to bid against myself, and the cupon upgrade was cleared off waitlist approx 24 hours before take-off.
One more observation about the instant upgrade offered (the 170€ offer that was live for just 24 hours and looked like someone went for it): The price difference between cheapest econmy ticket and a business ticket was (and still is) just 135€. So you only needed to do minimal research to realise the offer wasn't a great one. If people are jumping on these instant offers then no wonder Aegean prioritises selling upgrades instead of processing cupons.
Now there is 5 seats taken in business class, so my asumption is that besides me 2 others were on waitlist and got cleared at the same time.