I ran into this after an update from 16.04. I had a custom panel as well
but I found a way to show the notification panel again without resetting
the dconf configuration. I had three indicator-application.desktop files
(and I IIRC likewise as many probably competing running instances of
it):

/usr/share/mate/autostart/indicator-application.desktop
/etc/xdg/autostart/indicator-application.desktop
/usr/share/indicator-application/upstart/xdg/autostart/indicator-application.desktop

Only the last one seems to be the current one. I have removed (renamed)
the first two. I have not tested if that alone works already but edited
the remaining (third) file. I have added MATE to the list of shown-in
DEs:

OnlyShowIn=Unity;MATE;

After a reboot the new notification popped up where it is supposed to
including all expected apps.

** Also affects: indicator-application (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: network-manager-applet (Ubuntu)
       Status: Confirmed => Invalid

** Also affects: ubuntu-mate-settings (Ubuntu)
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/1754458

Title:
  nm-applet symbol not displayed on mate (18.04)

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