There are seven security updates through July 2017, since El Capitan 10.11.6 was released. There are just two requirements to receive them in the Updates tab of the Mac App Store:
- OS X 10.11.6 is installed
- The Mac App Store System Preference is configured with these checked:
- Automatically check for updates
- Install system data files and security updates
These settings allowed me to be automatically notified in the Mac App Store Updates tab when these security updates were released. Safari 11 was in Security Update 2017-003 released in July.
If you review your installation history ( menu : About This Mac : System Report... button : Software : Installations, you will see what Security updates have been installed. Mine appears:

You can obtain the missing Security Updates for El Capitan 10.11.6 directly from Apple's Download site, and by specifying “Security Update 2016-001.” Make absolutely certain that you choose those for El Capitan, and install all of them in numeric order.