If your going to be covering the frame with nylon or polyester it probably doesn't matter for strength because the skins will shrink and hold the frame tight and solid. If your planning on skinning the kayak with a looser fitting skin, such as canvas, then the mortise and tenon might work better. The mortise and tenon would allow the frame to flex and maintain a strong joint. I did my frame with mortise and tenon joints, from Chris Cunninghams book, and it took some extra time but was very rewarding.