Yes, protecting the connection and providing a few miles would be the only reason to make this worthwhile to me. I often continue by ferry (even though there are several ATH-PAS flights) as the prices are crazy due to the ATH airport tax and there is often 12+ hours wait (in the winter when I travel most).

The Hellenic Seaways (Now part of Attica/Blue Star) SeaSmiles loyalty scheme is not that bad actually. It's almost impossible to earn status - I think you need something like 30 round-trips in a year from Piraeus to the Cyclades to even earn Silver, but, even without status, you basically get one free trip for every ten you take, so that's OK. There are no availability blackouts at all on the free trips either.