As you may know, the Link Manager was removed in WordPress 3.5. For most people, this went unnoticed, since it wasn’t heavily used and basically was a relic from the past. The admin sidebar item should be disabled on all new installs. However, for older sites that still had the default links entered (because who remembered to delete them?) the sidebar item still shows up on the side. Previously, a function to remove or hide those items had to be used. However, a simple update can now be written. Add the below code into your functions file and the link manager will never reappear.
note: for the stand-alone
update_option function, make sure to remove it after it has run, since you don’t want the site doing the check each time.