The effective thickness method is based on Boeing Proprietary documents and data, so you are unlikely to find anything in the open literature.
Higher fastener stiffnesses are not necessarily conservative. None of the published fastener flexibility methods are accurate; however, large differences in flexibilty values usually produce only relatively small differences in joint load distributions. But, if you are sizing a joint to zero MS using a single set fastener flexibility values, you are just kidding yourself that the MS prediction is accurate. Critical joints should be designed using a range of flexibilities giving a range of load distributions ("overlapping assumptions").
Further, if you are using an FE model of the joint, you need to calibrate the FE model idealization and stiffnesses using a single joint configuration so that it matches the closed form fastener flexibility equations. You cannot directly calculate stiffness values for the FE model from the fastener flexibility formula. The calbration must account for the type of elements in the straps (shells, solids), and elements used to model the fasteners (rigid elements + springs, beams, bars + springs, etc.)