GNOME Shell extensions have a uuid property; this key lists extensions which should be loaded. Any extension that wants to be loaded needs to be in this list. You can also manipulate this list with the EnableExtension and DisableExtension DBus methods on org.gnome.Shell.
The shell normally monitors active applications in order to present the most used ones (e.g. in launchers). While this data will be kept private, you may want to disable this for privacy reasons. Please note that doing so won't remove already saved data.