as I travelled a lot last spring in this region, I also talked a lot to persons working there for rail companies... and there are some changes maybe in the long distance connections as the rail track will be renewed between Thessaloniki and Alexandroupolis in Greece. also in the summer months, there are often more and other rail connections than in winter.
in 2008 you had a connection with change in Thessaloniki. right now you have to go up until Sofia and then to Athens or Istanbul.
when the connection via Thessalonik will be available again, you have always two trains leaving from Athens/Istanbul per day.
Istanbul - Thessaloniki - Athens
Dep. Istanbul 0830 | 2030
Arr. Thessaloniki 2250 | 0715
Dep. Thessalonik 0720 | 1015
Arr. Athens 1135 | 1515
Athens - Thessaloniki - Istanbul
Dep. Athens 2255 | 1315
Arr. Thessaloniki 0530 | 1815
Dep. Thessalonik 0715 | 1955
Arr. Istanbul 2130 | 0800
the supplements for night trains are in most Eastern European countries the same. In Greece the use of the IC and ICE trains can become expensive by the supplements:
for the night trains add EUR 25 per bed in a double bed cabin and EUR 50 for your own single bed cabin.
and one mistake I did in the past: one of the wagons leaving in Istanbul has written on it Pithion - use this wagon as this one will cross the Turkish-Greece border so that you have access to the Greece rail network.
this is my personal experience of the last times I travelled this route.
and by the way... Sofia can be nice ... it is cheap ... and when staying in Bulgaria, you can also have a trip to the Black Sea (Varna) - also with night train connection. really nice there !