[UPDATE]: Yosemite support has been added.
I can’t guarantee results, but this has seemed to work for me. The following commands disable the Apple App Store notifications that appear in OS X:
NCutil.py --remove com.apple.maspushagent NCutil.py --remove _SYSTEM_CENTER_:com.apple.storeagent
I believe removing the noticeboard and app store will also suppress notifications.
NCutil.py --remove _SYSTEM_CENTER_:com.apple.noticeboard NCutil.py --remove com.apple.appstore
Disable These Annoying Notifications With NCutil.py
Normally, you cannot disable these because they do not show up in the Notifications pane of System Preferences, so I decided to write a command line utility that would allow you to do this called NCutil.py.
Give a try and see if you get the same results.