A scarf joint may not flex exactly the same as unjointed wood. If you place a joint in a location where there is a lot of curvature at the sheer line, such as near a stem, it might create a flat or "hot spot" where the wood does not quite conform to the hull. I think it is fine to have joints on both sides of the canoe line up at the same spot, but if you need to scarf both inwales and outwales, I would recommend offsetting the joints on each side of the boat by a foot or more, if possible.
I know that many recommend using long scarf joints of 1:7 or 1:8 for strength, I have found that shorter scarfs of 1:3 or 1:4 work perfectly well. I think long scarfs are necessary when jointing thin panels together in order to get a sufficient bonding area for the adhesive or epoxy, but gunwales are thick enough to provide a very satisfactory bonding surface with shorter scarfs.
I try when possible to avoid having gunwale screw holes, or the holes for machine screws fastening thwarts or suspending seats from going through the scarf joints, although I have seen some recommend having a gunwale screw go through the center of the joint. If you use long scarfs you are probably going to have to accept having at least a gunwale screw go through the joint.