Partial threaded and fully threaded screws are not interchangeable for structural applications. If you have to perform calculations or testing in order to validate the joint, then they are not interchangeable. Fully threaded screws will have lower stiffness, and therefore change the load relation of the screw vs. the joint. Loosening and fatigue characteristics will vary depending on the manner in which the threads are rolled, meaning exact geometry of the threads, where the thread run out occurs along the shank, etc. Have you consulted any of the usual fastener references like Bickford & Nassar's Handbook of Bolts and Bolted Joints?