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.
https://forum.xfce.org/viewtopic.php?id=16436
https://forum.xfce.org/viewtopic.php?id=17218
Note: restarting panel is non-trivial for me, it is something I do everyday many times for my own reasons.