Generally I've done all security updates through the App Store, as these don't change the OS X version number. Today, I installed a security update, and upon reboot, my Mac with GTX 980 is black screened. After screen sharing into it, turns out the nVidia driver is disabled on purpose and somehow not compatible with my OS version, even though I'm using 10.10.2. This is incredibly stupid behavior and I will definitely not install any security updates again until I can obtain 100% verification that they won't cripple my machine just for fun. Beware of this update.