Hi again,
if anyone else stumbles over this behaviour:
You have to set ‘custom-fields’ in the ‘supports’ array of your custom post type for meta that has been registered via ‘register_meta’ to work with REST API.
https://github.com/WordPress/gutenberg/issues/5622
While I figured out the solution by myself in the end: thumbs up for NGG support and bugtracker staff answering quickly and very politely!
I’ll consider recommending our customers getting a PRO license for NGG after this good experience.
Have a nice day!
Jan