I mean if it’s the only time you can go you just gotta deal with the weather. It’ll be humid/hot, you may have to deal with typhoon weather which means places could close and trains could stop working. If you traveled northern Japan the temperature would be better but it doesn’t mean the typhoon won’t come there too. If you can wait for another time of the year, I would suggest fall or winter instead. It’s not as busy and the temperature is perfect (esp fall) for traveling around.