I assume you have looked into and taken care of any issues regarding entering Japan as an unaccompanied minor, so I won't ask about that. The legal age of an adult in Japan is 20.
As for mid-flight turbulence, it doesn't happen every time but it does occur. I just pop a "Less Drowsy Dramamine" before take-off and forget about it. Another trick to keep the stomach settled is to substitute ginger ale for whatever soda you usually drink. It really does help.
If turbulence is encountered, it usually doesn't last long. The pilots work hard to go around weather so as to give the passengers as smooth a ride as they can. I wouldn't be too concerned.
Japan is my favorite place to visit. Have a great time.