There really is a reason. Well, a couple of them, actually.
1. - Cheaper plywoods are laminated in such a way that there is more strength against breakage in the longer direction. More expensive plywood doesn't seem to have this problem. Flooring plywood is the cheaper stuff.
2. - Perpendicular spanning of floor joists helps to negate the varying relative heights of all the top surfaces of the joists. They do not often create a flat, level plane upon which to place flooring. If your joint in your first drawing happened to fall on a joist that was either high (or low) in comparison to all the others, you would have a very pronounced rise (or a dip) in that area of your floor. Going crosswise to the joists reduces the prominence of such a deviation.
