sorry for not responding for such a long time. I'm aware of the issue you
are describing and think due to the messed up world of notification areas
there is no future safe solution. GNOME Shell along with an incompatible
KDE upgrade both killed all cross-desktop environment safe solution.
This is why I decided for 1.11 to significantly simplify the tray icon support.
The idea is to isolate the code into a plugin that will not activate with GNOME
shell and to have a different plugin for GNOME shell. To prevent the problem
you describe hiding was entirely removed (but could be reimplemented in tge
GTK notification area plugin as an option.