It's not enough that there are "tons" of seats available for purchase....upgrades require specific upgrade availability, and cannot simply be processed to book you into any available "cash" seat. To process an upgrade, there has to be an open seat in the relevant booking class that is available for Aegean. I would caution that, unless you can see that a seat is available for purchase outright using miles in A3 Miles and Bonus, that there probably isn't a seat available for them to upgrade you into using miles (even if searching via some other airline's programme appears to indicate that that other airline sees availability).

Looking up how many seats ET is willing to sell for money is not relevant. It's probably more relevant to see if A3 can "sell" you a business class seat on the particular flight in question using Miles, to try and determine that they have access to a seat which you could then instead request for an upgrade. But I cannot guarantee you that even if they could "sell" you such a J award, that they could actually process an upgrade into that available space.

Redeeming outright into business is always a better use of miles. Between factoring in the (high) cost of an economy ticket in the relevant high-fare classes, and the (high) cost of miles required to process an upgrade, together with the uncertainty of whether you will actually be able to get the desired upgrade - it is a far, far better use of your time, money and miles to instead redeem outright into J, rather than rolling the dice and hoping that an upgrade is, or will become, available once you have purchased a more-expensive-than-otherwise-necessary economy class ticket. Using miles for an upgrade really only makes sense if you, due to work or other commitments, find that you already have a high-fare Y-class ticket that could be upgradeable. It is never advisable to specifically book such a Y-class ticket when your actual goal is to travel in the J cabin You may end up paying far more than you needed to to get an economy class ticket, and you may end up flying in economy, rather than in business as you actually wanted.