Damn, 2 years again - how fast time flies. Still, they do exist, dear people - things that last, things that survive eons as if they were moments, things that in their incomprehensible survival skills will still exist when mankind has utterly died out and the earth has burned up to sheer glowing ashes…
Things like bugs in Cubase.
haha- I think, it’s a widely held forecast, that the bugs will be the longest lasting survivors on our planet. 
More seriously - I don’t think that Cubase has a worse bug ratio than any other sufficiently complex piece of software.
Encountered that issue as well. I’ve made a junction from all 4 default vst2 paths to one single folder in another drive to free up space on system disk. I was so happy that I don’t have to change vst2 x64 path each time when installing plugin, all of them automatically dropped to one single folder. But then I’ve encountered issue when each time Cubase scans for new plugins it does it four times! Deleting those default vst paths from vst2 plugin settings could solve the issue but they keeps recovering each time Cubase starts.
Junctions I made:
mklink /J “C:\Program Files\Common Files\VST2“ “D:\VST64”
mklink /J “C:\Program Files\Common Files\Steinberg\VST2” “D:\VST64”
mklink /J “C:\Program Files\Steinberg\Vstplugins” “D:\VST64”
mklink /J “C:\Program Files\Vstplugins” “D:\VST64”
It works great except that 4 times scan issue cause it thinks that same plugins installed in each default folder.
So in order to solve that scanning issue I had to make separate folder for each default vst2 path on D: drive:
mklink /J “C:\Program Files\Common Files\VST2“ “D:\VST64\1”
mklink /J “C:\Program Files\Common Files\Steinberg\VST2” “D:\VST64\2”
mklink /J “C:\Program Files\Steinberg\Vstplugins” “D:\VST64\3”
mklink /J “C:\Program Files\Vstplugins” “D:\VST64\4”
Not the best solution but at least it works. IF only Cubase did not reset all those deleted default VST2 path in it’s settings that could solve all the issues.