Have you also imported the python apt module with "import apt"? Eg:
>>> import apt, apt_pkg
>>> email = apt_pkg.Config.Find("Unattended-Upgrade::Mail", "")
>>> print email
You should notice the loading of the apt module as it prints a warning
message about the API not being stable yet.
If that doesn't work then you could try a full dump of the config:
apt-config dump | grep -i mail
--
does not send mail despite Unattended-Upgrade::Mail set
https://bugs.launchpad.net/bugs/136720
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