macOS update closed all my applications?
You will normally be prompted to install updates as they are detected. However if you were away from your computer you may not see those notifications. Also if you delay them enough times they will eventually be installed for you. Lastly if the updates are detected overnight they may be installed right then as well. This is usually done sometime after 3 a.m.

You can go to  → System Preferences → App Store and uncheck the following:


Install app updates
Install macOS updates
Install system data files and security updates




This will keep macOS from installing updates, quitting apps and/or restarting your system without asking you first.

You will still be notified when updates become available, and offered the choice to install them.