I managed to workaround the trouble :
$ sudo rm /usr/bin/thunderbird

The facts are that :
- gnome-default-applications-properties looks for mozilla-thunderbird and 
thunderbird executables and show corresponding entries in the menu ("Mozilla 
Thunderbird" and "Thunderbird"),
- thunderbird package install both /usr/bin/mozilla-thunderbird and 
/usr/bin/thunderbird links (the target is ../lib/thunderbird/thunderbird for 
both).

Usefull commands to understand the facts :
$ strace gnome-default-applications-properties 2>&1 | grep thunderbird
$ dpkg --listfiles thunderbird

-- 
After installing Thunderbird, preferred applications shows both "Mozilla 
Thunderbird" and "Thunderbird"
https://bugs.launchpad.net/bugs/373167
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