I have edited the KoboRoot.tgz file.
The hypen files are in \KoboRoot.tgz\KoboRoot20.tar\.\usr\local\Kobo\hyph enDicts\
After updating something there I have copied the tgz file again in the .kobo directory and the Kobo did an update.
The German file I use is this one:
http://www.j3e.de/myspell/hyph_de_OLDSPELL.zip
I have added the three lines
UTF-8
LEFTHYPHENMIN 3
RIGHTHYPHENMIN 3