OK: Although there was not a single plugin loaded in the projects, I started Nuendo with [Ctrl+Shift+Alt] without third-party VSTs. And now everything works.
I then went looking for the plugin and found the culprit plugin: It was iZotope RX11 (Standard). After uninstalling everything worked. Keyboard commands and everything worked again.
I then reinstalled iZotope RX11 - and the focus error appeared again. After installing iZotope RX Standard I have the malfunction again.
So the culprit is clearly iZotope.