I have also tried to let the systemd unit file for this service WantedBy the 
umount.target.
According to the systemd documentation that should make it run before the 
filesystems
are unmounted, but apparently that doesn't work. systemctl list-dependencies 
still shows
that the unattended-upgrade.service reverse depends on the shutdown.target.

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https://bugs.launchpad.net/bugs/1654600

Title:
  unattended-upgrade-shutdown hangs when /var is a separate filesystem

Status in unattended-upgrades package in Ubuntu:
  New

Bug description:
  The systemd unit file unattended-upgrades.service is used to stop a running 
unattended-upgrade
  process during shutdown. This unit file is running together with all 
filesystem
  unmount services.

  The unattended-upgrades service checks if the lockfile for unattended-upgrade
  (in /var/run) exists, and if it does, there is an unattended-upgrade in 
progress
  and the service will wait until it finishes (and therefore automatically wait 
at
  shutdown).

  However, if /var is a separate filesystem, it will get unmounted even though 
/var/run
  is a tmpfs that's still mounted on top of the /var/run directory in the /var 
filesystem.
  The unattended-upgrade script will fail to find lockfile, sleeps for 5 
seconds, and
  tries to check the lockfile again. After 10 minutes (the default timeout), it 
will finally
  exit and the system will continue shutdown.

  The problem is the error handling in 
/usr/share/unattended-upgrades/unattended-upgrade-shutdown
  where it tries to lock itself:

      while True:
          res = apt_pkg.get_lock(options.lock_file)
          logging.debug("get_lock returned %i" % res)
          # exit here if there is no lock
          if res > 0:
              logging.debug("lock not taken")
              break
          lock_was_taken = True

  The function apt_pkg.get_lock() either returns a file descriptor, or -1 on an 
error.
  File descriptors are just C file descriptors, so they are always positive 
integers.
  The code should check the result to be negative, not positive. I have 
attached a patch
  to reverse the logic.

  Additional information:

  1)
  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04

  2)
  unattended-upgrades:
    Installed: 0.90ubuntu0.3
    Candidate: 0.90ubuntu0.3
    Version table:
   *** 0.90ubuntu0.3 500
          500 http://nl.archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
          500 http://nl.archive.ubuntu.com/ubuntu xenial-updates/main i386 
Packages
          100 /var/lib/dpkg/status
       0.90 500
          500 http://nl.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          500 http://nl.archive.ubuntu.com/ubuntu xenial/main i386 Packages
  3)
  Fast reboot
  4)
  Very slow reboot (after a 10 minutes timeout)

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