How do I disable App Store notifications when auto-updating software?
I don't have any apps installed to try this with, but this looked like it might work. The solution is for Mountain Lion, not Mavericks, so it may have changed.

How do I turn off App Store notifications in Mountain Lion


  I just discovered the missing solution here:
  http://osxdaily.com/2012/11/15/stop-software-update-mac-os-x/
  
  You can selectively disable notifications about specific software
  updates you don't care about (like useless App updates) by
  control-clicking the update inside the App Store to reveal a hidden
  "Hide Update" option.
  
  This is best for those who want to keep Notification Center active for
  all its other uses (calendar alarms, etc.) and who also want to be
  notified about critical software updates. It should permanently mute
  notifications about certain software updates (until that software
  comes out with a new update).