After digging a bit deeper I found out that that the default configuration of 
/etc/apt/apt.conf.d/50unattended-upgrades is exactly the same as I had in my 
experiment i.e.
- the ${distro_id}:${distro_codename}-security origin is ENABLED
- the ${distro_id}:${distro_codename}-updates and others origin are DISABLED

The consequences are the following. A fresh install of Ubuntu LTS e.g.
16.04 keeps installing the *-security updates, but not the *-updates
ones. The number of packages with new versions in *-updates repository
keeps growing unless somebody installs them manually. It is a couple of
clicks, but still many people never do it. As the list of upgradable
packages grows, unattended-upgrades get slower and slower to the point
that it may take hours to complete.  Effectively, the automatic updates
may no longer work at all depending on how a given system is used. Also
the user experience gets worse with CPU busy executing the unattended-
upgrades script.

All in all, I consider it a serious issue that requires attention.

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Ubuntu.
https://bugs.launchpad.net/bugs/1396787

Title:
  checking trust of archives eats a lot of cpu

Status in unattended-upgrades package in Ubuntu:
  New

Bug description:
  (System: Ubuntu 14.04, up to date packages)

  I noticed that unattended-upgrades spends a significant amount of time
  in phases where it runs at 100% cpu. On a slower machine (core 2 t7200
  2GHz) this goes on for minutes rather than seconds. This interferes
  with using the machine for other tasks.

  Using the --debug option to unattended-upgrades shows that the program
  outputs a lot of lines like the following during these 100% cpu
  phases:

  matching 'a'='trusty-updates' against '<Origin component:'universe'
  archive:'trusty-updates' origin:'Ubuntu' label:'Ubuntu'
  site:'de.archive.ubuntu.com' isTrusted:True>

  From this output I guess the operation executed is not so complicated
  that it should require so much cpu power. ??

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: unattended-upgrades 0.82.1ubuntu2
  ProcVersionSignature: Ubuntu 3.13.0-40.69-generic 3.13.11.10
  Uname: Linux 3.13.0-40-generic x86_64
  ApportVersion: 2.14.1-0ubuntu3.5
  Architecture: amd64
  Date: Wed Nov 26 21:53:57 2014
  InstallationDate: Installed on 2014-08-28 (90 days ago)
  InstallationMedia: Kubuntu 14.04 LTS "Trusty Tahr" - Release amd64 
(20140416.1)
  PackageArchitecture: all
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=de_DE.UTF-8
   SHELL=/bin/bash
  SourcePackage: unattended-upgrades
  UpgradeStatus: No upgrade log present (probably fresh install)

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