Hi JB
It's been a while since I've messed with this, but here's what I found out a few years back.
There are two files that contain the tag structure.
A "user" file: C:\Users\[Username]\AppData\Local\Mixbus7\plugin_metadata\plugin_tags
And a "global" file: C:\Program Files\Mixbus7\share\ardour7\plugin_metadata\plugin_tags
If you open the "user" file in a text editor, you should find that it contains all the plugins you've personally tagged.
The "global" file, on the other hand, contains a lot of pre-tagged plugins, that you may or may not own. It's due to the contents of this "global" file that you see those empty tags in the plugin structure in Mixbus.
Before you proceed, make a backup of both of the plugin_tags files - just in case...
To remove all the unwanted tags in your plugin structure in Mixbus, simply replace the "global" file with a copy of the "user" file so that the two files are identical, containing only your own tags. (It may also work by just renaming the "global" file something like "plugin_tags_off", or simply deleting the contents of the file, but I haven't tested all the options thoroughly enough to tell if it makes a difference, or whether there might be some undesired side effects to either of them - hence the backups
)
Enjoy your uncluttered plugin structure!