EntityFieldQuery and "legacy" nodes
Although EFQ is a good tool, it starts with the assumption that you are querying about a field value.  It does not do the join because it is more efficient to get what you want the way it does it.  For you legacy nodes, I think you should do a legacy Dynamic Query.  This way you can specify a Left Join to get a result set that includes nodes with NULL/absent entries in the field table.

$query = db_select('node', 'n');
$query-&gt;leftJoin('field_data_field_myfield', 'f', 'n.nid = f.entity_id');
$query-&gt;condition('f.value', array('myvalue', NULL), 'IN')
  -&gt;condition('n.type', 'my_content_type');


Joins in the dynamic query method.