The S60 Notes application stores all the notes in a single file. On S60 2nd and 1st Edition you can access the file. On S60 3rd Edition and late, the file is in a private subdirectory which is not accessible without AllFiles capability (privilege).
The file format is not published.
Use the S60 C++ APIs to get to the actual notes and export them to whatever format you wish. You can also try to locate existing programs that already does it for you.