After recently upgrading a CRM2013 test system in one of my VMs I discovered that I couldnt change any security settings as the option in Settings had completely disappeared. I thought for a while I was going mad, but no it should definitely have been there.
It turns out the fix was really easy to do:
First create a new solution, and add the sitemap to it.
Open the zip file and pull out the customizations.xml file and open it in your favourite editor.
Search for the file for Group Id="System_Setting"
<SubArea Id="nav_administration" ResourceId="Homepage_Administration" DescriptionResourceId="Administration_SubArea_Description" Icon="/_imgs/ico_18_administration.gif" Url="/tools/Admin/admin.aspx" AvailableOffline="false" />
<SubArea Id="nav_security" ResourceId="AdminSecurity_SubArea_Title" DescriptionResourceId="AdminSecurity_SubArea_Description" Icon="/_imgs/area/Security_32.png" Url="/tools/AdminSecurity/adminsecurity_area.aspx" AvailableOffline="false" />
<SubArea Id="nav_datamanagement" ResourceId="Homepage_DataManagement" DescriptionResourceId="DataManagement_SubArea_Description" Icon="/_imgs/ico_18_datamanagement.gif" Url="/tools/DataManagement/datamanagement.aspx" AvailableOffline="false" />
And between the nav_administration and nav_datamanagement items insert the highlighted block.
Save the file.
Insert the file back into the zip file.
Reimport the solution and publish it.
It might be best to do this out of hours if its a production system as I had to perform an IISRESET before the icon came back for me.