In the meanwhile I have found the following:
1. Every used file (linked from course page, or used within e.g. questions) is indeed converted to the new storage system. BUT in addition to this they are also put into Legacy files. I do not really know the reason for this, see the next point.
2. Putting all files into Legacy files can be prevented following the step in the 2nd post of legacy files ..."Why won't you die!!?" All used files (links, images in questions, etc) work as expected, no need for Legacy files
3. The Legacy files are is still created, although it is empty. This can be removed by directly editing the database (at least I haven't found other methods), just run
UPDATE `mdl_course` SET `legacyfiles`=0;