Run xfce4-panel -q && xfce4-panel (restart XFCE panel), sys-net and sys-whonix trays do not appear again, while other trays (and all other objects in panel) appear normally.
I have searched much for this, what I found is only killing ayatana or uninstall it, but it is not present in Qubes.
Seconded.
I noticed this panel behaviour and can add another observation, all on R4.2 up-to-date:
If I log out, then log in again, the sys-whonix tray (the padlock) does not appear. In this case, sys-net’s tray does reappear, though.
Minor annoyance but still… restarting sys-whonix just to get the padlock seems unnecessary.