That files is provided by apt not unattended-upgrades.
$ dpkg -S /etc/cron.daily/apt
apt: /etc/cron.daily/apt
** Changed in: unattended-upgrades (Ubuntu)
Status: New => Invalid
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https://bugs.launchpad.net/bugs/1374913
Title:
/etc/cron.daily/apt missing in 0.76ubuntu1
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