Thanks a lot JMarc and Günter for your interesting explanations! I've tried now the LatinModern font which works indeed better. Also changing the encoding to OT1 worked (if I don't want to search for Umlauts ;-) ) Sorry that I have posted my question to lyx-devel and not lyx-user, but the reason was to suggest to make it possible to deselect the package fontenc. And I still think that all packages should be deselectable. But my specific problem for the moment is solved, so thanks a lot.
- Sebastian