I'm using popper mail notification, which integrates into the messaging applet, therefore I have no use for the default message indicator entries. Is there a way to hide/remove them?
I already disabled the thunderbird unity integration add-on.
/usr/share/indicators/messages/applications/ as explained here, are just text files containing path to desktop file. You can blacklist them per-user:
cp /usr/share/indicators/messages/applications/* ~/.config/indicators/messages/applications-blacklist/