I remember a similar discussion to this about a year ago. All I could find was this:
Kiwi.com fake flights?
This was a "proper" charter flight with a 4-digit flight number and not listed at all by A3 themselves. I
assume this is what they are referring to when they say miles cannot be earned on "IT flights". I think there was another thread where somebody booked a seasonal flight from one of the islands to a non-regular destination in N Europe and it was in a different booking class (maybe N?) which is explicitly stated as not earning. I can't find that thread though. Maybe somebody else remembers.
EDIT: Ah this is what I was thinking of. The issue here was a 'J' class fare that couldn't be upgraded but the same principles may apple. One poster (reply 3) states that J class (despite being listed as earning) do NOT earn as they are IT fares.I don't know if there is a similar issue with the class(s) you are booked into.
Be careful if booking with Expedia (and wanting to upgrade using vouchers)
Also scroll down to reply 19 - A reply from Aegean saying that a fare didn't earn miles becase there was no fare charged - just taxes and that normal tickets in that same booking class would earn. This ties in with what Xandrios said above.
Sorry, nothing definitive, but more info for you to ponder...