Hello,
as announced my findings so far.
To look into one of the DBs, I'm using SQLite Manager for Firefox:
https://code.google.com/p/sqlite-manager/
Schemaspy can be used to get an overview:
http://schemaspy.sourceforge.net/
There is also an schema for the Kobo DB here:
http://kobodb-schema.sourceforge.net/index.html
But this is version 52, while my DB claims to be 101 - quite a gap.
The "Bookmark" table seems to contain the notes:
column "text": Marked text
column "Annotation": The note added ot the bookarm/marked text
Regards
Martin