Based on some of the comments above, I came across this:
… and this quote in particular:
Our developers found a problem in OS X
On Mac computers, one might also observe that some plug-ins that end up on the blacklist appear to have worked perfectly fine in previous Cubase versions.
The reason is that our developers found a problem in OS X 10.11 (El Capitan) and previous versions which cause plug-ins compiled with an older Objective C Runtime version to become unstable.
Using these plug-ins causes Cubase to behave erraticly on the mentioned OS X versions. The symptoms are random hangs, crashes and very often it causes crashes when you close Cubase. For the user there’s usually no visible connection that those problems are being caused by a plug-in.
With macOS 10.12 (Sierra), Apple fixed that problem from the OS side. We also work closely together with plug-in developers, so if still supported, affected plug-ins might receive an update to fix that issue on OS X 10.11 and lower."
So maybe there is some overall benefit. It would also explain why so many plugins had trouble with this OS update come to think of it.
So I took the plunge and upgraded to Sierra. I have not tested a lot of other software, but I can report that my blacklist problem with Cubase is GONE. Only plugins that fail (besides any 32 bit ones) are all of iZotope 64 BIT VST3 plugs. (However, their VST2 stuff passes.) The plugin scan is a lot faster too.
OK. THAT problem gone, now let’s go check out the rest.
Thank you everyone for your help!