Yes they show up. But without those invisible by blender fonts. So You are right fonts are linked and not actually in that directory.

After run this command:

Other programs see those fonts without problem.

When i select a different font directory (no windows/fonts) Blender see all the fonts, both TTF and OTF format. And loads them without a problem.
When i right click on a font (which the blender can not see in the windows/Fonts directory) and click install (or install for all users) font appears in windows/fonts directory but blender do not see him. But in different directory he sees without a problem.
All installed fonts are in Windows/Fonts directory.

1 - Folder - Windows/Fonts in Directory Opus on Windows 10

In User preferences i have set to Windows/Fonts folder.
Blender see only default fonts.
All font blender dont see is ttf format.