There's surely a chance that I might be mistaken, but it does seem like
it comes from ibus-gtk.
In the ibus source package, you can find the string that gets displayed
in ui/gtk3/panel.c, line 3130:
"""
_tmp0_ = notify_notification_new (_ ("IBus Update"), _ ("Super+space is
now the default hotkey."), "ibus");
"""
It only gets displayed the first time you log in, which is perhaps why
you couldn't reproduce it.
However, it's easy to observe when booting any GTK-based Debian Live media.
You can boot up
https://cdimage.debian.org/cdimage/weekly-live-builds/amd64/iso-hybrid/debian-live-testing-amd64-xfce.iso
as an example.
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