This has been discussed many many times, and there seem to be two camps! One who don't care what others wear, and another who believe there is a dress code for flying, especially in the more expensive classes.

My opinion is of the first group - wear what you feel comfortable in, and in my experience the flight staff (who are the people who matter in this case) really will not care how you're dressed.

Just one thing though... although you say you're wearing shorts because you're travelling to Japan because it will be hot, the temperature on the plane might be quite cool. But if you're more comfortable in shorts, just wear them and enjoy your trip!