Thanks. I’m marking this as a solution based on your confirmation, and it’s good to know in case I ever need to try this sort of test again. As it is, creating a new admin account, doing all the scanning fresh (when some older plugins put up prompts, and I’ve got thousands of plugins that have to get scanned), is sufficiently painful that I really hope not to need to do this again (especially since my main account is already an admin user).
Something to absolutely avoid, sorry. In several places in this forum, it’s been clearly stated that using Cubase with administrator rights/account is counter-productive, for different reasons. And I’m even wondering if the scan issue you have couldn’t be related.
Beside this, using an administrator account with an eventual active internet connection is searching for serious security issues… 
I think you are misunderstanding. I am not running Cubase (or any other applications) “as administrator”. That would be where issues with Cubase, as well as extra security issues, would arise.
Rather, my user account has admin privileges, which means that, when I need to install software, I can. Windows prompts me as to whether to allow the installation program to “make changes to (my) device”, and, if I say okay, it will run the installation program. If I don’t, it won’t install the software since, for example, it can’t update the registry, install files in protected directories, etc.
OK, sorry for the misunderstanding… 
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Just had a corrupt user profile to deal with on Windows 10 (first time in 10 years!), had the same issue as others, all VST3 plugins showing when running Cubase 15 as admin, but not otherwise (even though the user is an admin).
I deleted the Cubase 15 folder in the Roaming directory (so preferences gone), still wouldn’t scan, doing what you suggested worked, thanks for this!
Perhaps Steinberg can implement something to overcome this as deleting preferences does not fix the issue, in my case, I only had Halion SE show up even though there were other instruments within the Steinberg folder, very odd to only pick up one VST3!