Default sort on admin columns with meta date hides draft posts with empty date value

I too was struggling with this (only I was sorting by a text-based meta value). Here’s what seems to have fixed the problem:

$meta_query = array( 
    'relation' => 'OR',
    array(
      'key' => 'property_reference',
      'value' => false,
      'type' => 'BOOLEAN',
    ),
    array( 
      'key' => 'property_reference',
      'compare' => 'NOT EXISTS',
      'value' => '', //have to set value due to bug: core.trac.wordpress.org/ticket/23268
    ),
    array(
      'key' => 'property_reference',
    )

  );

  $query->set( 'meta_query', $meta_query );  
  $query->set( 'meta_key', 'property_reference' );      
  $query->set( 'orderby', 'meta_value' );

…where property_reference is my custom field.