Yep, 6 is the hughest level of security check, but there are subdivisions inside that level. One is the lowest security level (Israeli citizens and people bearing a Jewish surname). The search you went through is the routine search for anyone who may have been in contact with Palestinian people, and for any aid worker and journalist, so it's pretty common. Some people will tell you it's for security reasons, others that's it more about harassing anyone who might have had a peek at how life looks like in Occupied Palestinian Territories.
As you said, just remain patient and everything will be fine. Though the experience can be a bit traumatizing the first time.