I think booking with a travel agent might be the reason for that button missing, yes.
There's also an 8 euro fee, in addition to the cost, when calling in to prepay additional baggage. This is taken from the same link I referred you to (all the way down the page, under "IMPORTANT NOTES").
- Should you wish to prepay for additional or overweight bags through the Aegean call center, in case you have already purchased your ticket you will be charged €8 per passenger.
I guess it almost won't be worth it to even bother then, with the extra fee and considering the cost of the phonecall as well ...
Snacky