Mac OS 10.8 and older had a system preference pane named Software Update, and that’s where you would go to view/apply updates from Apple. This included things like operating system patches and security updates.
Apple removed the Software Update system preference pane in Mac OS 10.9, and replaced it with one named App Store. This was linked to the Mac App Store app, and applying Apple updates confusingly could not be done directly in the system preference pane.
Mac OS 10.14 will be bringing back the Software Update system preference pane, and removing the dependence on the Mac App Store app. I’m guessing this is because Apple is completely overhauling the Mac App Store’s look and feel, and the confusing Apple Updates section never really seemed to fit.