You need to edit the
tk-shotgun-folders app settings in your config to list which permission groups are not allowed to use the app.
For example, you could have:
settings.tk-shotgun-folders: deny_permissions: ["Artist", "Manager"] deny_platforms:  location: "@apps.tk-shotgun-folders.location"
Which would stop artists and managers from seeing that app.
Note that this won’t stop users from being able to create folders, however, as when they launch the DCC’s it will automatically create the required folders for the context they are on.