iMac won't restart for Security Update 2016-001 10.11.6 I have been having problems when I go to install the above update. I click 'restart' to allow the computer to update but it never does. The dock and desktop wallpaper remain but the menu bar at the top and all icons on the desktop disappear. 

I have the same problem exactly whenever I go to shut down the computer. I click shut down and again the dock and background stay but everything else vanishes. It is as if it has only partially gone through the process. 
Any help would be greatly appreciated.
Your problem is in no way related to Security Update 2016-001.

When your Mac want to terminate a system update, it should go through
a normal Restart... as the one you see in  &gt; Restart....
And to achieve this restart it must terminate correctly all the
processes actually running.

Your actual problem is caused by one process which refuse to exit correctly.

The first and easiest way to diagnose which process is the culprit
consists of using the combination to force quit any ill behaving
application:

command ⌘option ⌥esc

If my hypothesis is correct you might see a typical application
flagged as not responding. This mean that this process became deaf
stupid and won't hear the signal sent by the system to tell it to exit.
In this case, just kill it with the Force Quit button.