There are two components to the problem as I read it:
- How to project the shapefile into the desired projection
- Recurse a directory structure projecting every shapefile you encounter.
In terms of the first - I'm unfamiliar with the those projections but since one is a transverse mercator (spatial reference org) and the other is lamberts equal area and are on different datums you will have to use the correct transformation to preserve the accuracy of your coordinates. When in doubt project the greek grid into UTM first as most national survey offices will have a documented procedure to get their national grid into UTM and it may make it easier to identify the steps involved.
Second recursing a directory structure for this work is fairly straightforward in python. Check the documentation on the builtin os module - particularly you will want os.walk. You can use this to action your projection routine on every shapefile in the entire tree under the folder you use as argument to os.walk. Very powerful and timesaving.