Link by Element ID Does Not Work

I am not sure I understand what you are trying to do... Can you elaborate on how to reproduce this on our demo page, step by step? Thanks!

The link plugin doesn't search for any element with in id, it just search for anchors ("a" or fake images) and then lists them (of course they won't have id if you have created the anchors with the editor because it only inserts the name attribute)

extracted from link.js

      // Find out whether we have any anchors in the editor.
      var anchors = retval.anchors = [],
         i, count, item;

      // For some browsers we set contenteditable="false" on anchors, making document.anchors not to include them, so we must traverse the links manually (#7893).
      if ( CKEDITOR.plugins.link.emptyAnchorFix )
      {
         var links = editor.document.getElementsByTag( 'a' );
         for ( i = 0, count = links.count(); i < count; i++ )
         {
            item = links.getItem( i );
            if ( item.data( 'cke-saved-name' ) || item.hasAttribute( 'name' ) )
               anchors.push( { name : item.data( 'cke-saved-name' ) || item.getAttribute( 'name' ), id : item.getAttribute( 'id' ) } );
         }
      }
      else
      {
         var anchorList = new CKEDITOR.dom.nodeList( editor.document.$.anchors );
         for ( i = 0, count = anchorList.count(); i < count; i++ )
         {
            item = anchorList.getItem( i );
            anchors[ i ] = { name : item.getAttribute( 'name' ), id : item.getAttribute( 'id' ) };
         }
      }

      if ( CKEDITOR.plugins.link.fakeAnchor )
      {
         var imgs = editor.document.getElementsByTag( 'img' );
         for ( i = 0, count = imgs.count(); i < count; i++ )
         {
            if ( ( item = CKEDITOR.plugins.link.tryRestoreFakeAnchor( editor, imgs.getItem( i ) ) ) )
               anchors.push( { name : item.getAttribute( 'name' ), id : item.getAttribute( 'id' ) } );
         }
      }

Of course it would be better to provide all the elements with an id or remove that select box if it's not meant to be used.
This works for modern browsers:

      var doc = editor.document.$;
      if ( doc.querySelectorAll )
      {
         var elements = doc.querySelectorAll('[id]');
         for ( i = 0, count = elements.length; i < count; i++ )
         {
            item = elements[ i ];
            if ( item.nodeName != 'A' )
               anchors.push( { name : item.getAttribute( 'name' ), id : item.getAttribute( 'id' ) } );
         }
      }

I've created http://dev.ckeditor.com/ticket/8982 so that the patch doesn't get lost, but I don't think that it will be applied because then people with old browsers will say "hey this new feature doesn't work in my browser and our company can't upgrade, so you must write the code to support this shitty browser"