Okay, I have identified the problem.

update-notifier supports a mode called "auto-launch". When it discovers
new updates and auto-launch mode is enabled, it doesn't notify the user
at all, but launches update-manager instead. If update-manager detects
important security updates, it immediately displays a window
interrupting whatever the user was doing. (I suppose some people might
like this, but I find it very irritating.) On the other hand, if update-
manager detects only unimportant updates, it remains minimized, which
might mean it remains nearly or entirely invisible depending how the
user's desktop displays minimized windows. It is very easy to miss on
Xubuntu, and probably almost every other desktop other than Unity.

Some time between Ubuntu Raring and Saucy, somebody ripped out update-
notifier's checks for whether the user's system has "auto-launch" mode
enabled, forcing everyone into auto-launch mode instead. In one case,
they even went so far as to leave this comment in place of the working
code:

// everybody wants auto-launch mode

I'm guessing that the author of that comment assumed that the whole
world uses Unity, which is clearly a mistake.

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https://bugs.launchpad.net/bugs/1246364

Title:
  update-notifier does not show a tray icon in xubuntu 13.10

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