Guys, I think I have solved the issue. What helped me, was @Chaezaa s comment about Node 42.
I scanned the files for that number, and there was a “FLAP_RATIO” group, which hat this node as its child more than once. In a lot of planes that is the case. Removing these additional references made the models working again.
In total, 14 planes are affected.
As a hotfix, I have made this: https://de.flightsim.to/file/21499/invisible-ivao-aircraft-after-wu6-hotfix
which you can drag and drop in your community folder to overwrite the IVAO-xcsl. It replaces only the corrupt files. I have also contacted IVAO to incorporate those adjustments into their files so that this should become obsolete in a while.
Cheers.