Default join on collection is an inner join so if you are doing that :

$myCollection()->addAttributeToFilter('my_attribute', array('null' => true));

.. you will find no entries

If you want to change the default inner join to a left join you just have to add ‘left’ as the third parameter of the addAttributeToFilter method :

$myCollection()->addAttributeToFilter('my_attribute', array('null' => true), 'left');

and now it works…

Here is the prototype of the corresponding method in Mage_Catalog_Model_Resource_Product_Collection :

public function addAttributeToFilter($attribute, $condition = null, $joinType = 'inner')

We can see that inner parameter is used by default

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