Ok, so what you call 'notification' seems to be in fact the application
itself opening (you still didn't include any screenshot showing a
notification so let's assume it's a vocabulary error)

could you 
$ killall update-notifier
$ update-notifier --debug-updates

ANd copy the log there?

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https://bugs.launchpad.net/bugs/1817559

Title:
  update-manager ignores its own settings completely

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