Why are Rhino5 and Rhino6 grasshopper plugins using the same paths ? This causes trouble when some components are not fully compatible.
Suggestion: If there’s a good reason for the current strategy (identical paths), perhaps you could introduce a new settiing - the plugin path - for Rhino6, with the old Grasshopper path set as default?
It’s legacy mostly, with a layer of poor or unmade decisions.
To hide a GHA file from Rhino5, put it in the %appdata%\Grasshopper\6\Libraries\ folder.
To hide a GHA file from Rhino6, put a second file with the same name but the extension *.no6 next to it.
In an upcoming Rhino6 service release, there will be a command called _GrasshopperIgnorePlugin which automatically places that no6 file next to plugins you don’t want, but for the time being you have to do it manually.