I also prefer a single file, FWIW, but that's one question where I don't think there's any universal answer.
But as to the rest, I've never seen a file that was too big or had too many waypoints, so I'd err on the side of including all the ones you have. Those whose devices have a limit can always downsample, and the worst a device will do with waypoints is ignore them, whereas if the information isn't in there then there's no way to put it back.