My lad,the most part of ANY merchant fleet at any given time is mostly OUT of its country's national waters at any given time,because of the very nature of its business(This must also be the reason why the Norwegian merchant navy wasn't caught).This makes it more probable that they weren't caught by the Germans.Is this a proof?No,it is an assumption.After all,yours is an assumption too.Do YOU have proof that most were caught by the Germans?Uboat net says they helped a lot during the war.One of the above links speaks of hundreds sunk..Maybe Uboat net has more details on ships sunk,i don't have the time to search it.I brought up that incident of 1944 as indicative,to show that U-boats apparently did shoot at Greek ships,which is another hint (while we have no opposite proof,but an assumption).
Another hint i have found :
There were 450 merchant ships owned by Greeks before W.W. II. Out of those Aristotle said 410 were sunk during the war. The official count was 360.
http://www.whale.to/b/hitler.html
Of course you are free to do your own historical accuracy as you wish.Fortunately,history isn't written in forums by gamers.I just thought to join the discussion and help to the issue.
Regards
P.S:Although you might think most of what i wrote as irrelevant,i think it might be not,when a country still has an exile goverment and assets still flying the national flags and markings.I would consider THAT the true greek gov and navy/army/airforce and not the ones under a swastika.The next in order after the King that could be considered as legitimate chief of the Greek state,was the PM,who though shot his brains when the Germans were at the outskirts of Athens.So even legally,when captured ships were confiscated,they passed automatically to Italian and German ownership and i wouldn't consider that part of the greek navy anylonger.What i know is that they left alone fishboats.For the rest,i don't even know if there was even greek flag(or only greek) on the confiscated ships.Do you?