In field_sql_storage_field_storage_query, any condition on a field's column excludes entities with a NULL value for this column

Because field_sql_storage_field_storage_query uses INNER JOINs instead of LEFT JOINs, any condition on a field's column excludes entities with a NULL value for this column

Because of this, using the "NOT IN" operator in EntityFieldQuery::fieldCondition restricts the results to only the entities with a value for the field. For instance, on an SQL field storage the following query will only return the nodes with a least one tag but not one in $tids. It will not return node without any tag.

$results = $query->entityCondition('entity_type', 'node')
  ->fieldCondition('field_tags', 'tid', $tids, 'NOT IN')
  ->execute();