class Tx_MyExtension_Domain_Repository_FooRepository extends Tx_Extbase_Persistence_Repository {
    public function initializeObject() {
        $querySettings = $this->objectManager->create('Tx_Extbase_Persistence_Typo3QuerySettings');
        $querySettings->setRespectStoragePage(FALSE);
        $this->setDefaultQuerySettings($querySettings);
    }
}

/**
 * Constructor of the repository.
 * Sets the respect storage page to false.
 * @param Tx_Extbase_Object_ObjectManagerInterface $objectManager
 */
public function __construct(Tx_Extbase_Object_ObjectManagerInterface $objectManager = NULL) {
    parent::__construct($objectManager);
    $this->defaultQuerySettings = new Tx_Extbase_Persistence_Typo3QuerySettings();
    $this->defaultQuerySettings->setRespectStoragePage(FALSE);
}

http://forge.typo3.org/projects/typo3v4-mvc/wiki/Default_Orderings_and_Query_Settings_in_Repository

With this method you can overwrite the default settings.
So extbase will ignore the storage pid.

TYPO3 Extbase Repository ignore storage pid

PHP