If you wan’t automatically make all simple products which are configurable options of configurable products to be hidden in catalog, you have to change their visibility to “Not Visible Individually”.

Next SQL-query will help you with that task.

UPDATE
`catalog_product_entity_int`
SET 
`value` = 1
WHERE
`attribute_id`=(SELECT `attribute_id` FROM `eav_attribute` WHERE `attribute_code` = 'visibility')
AND
`entity_id` IN (SELECT `product_id` FROM `catalog_product_super_link`);