September will still be very hot. As for typhoon risk, it's intermittent - for 2 days you will likely not see any severe weather, but if they do show up, they will wreak havoc on your plans. 2 days doesn't give much margin for change if needed. September is the busiest season for typhoons (and hurricanes) but only a few make it up to the Japanese mainland.

Otherwise the weather won't necessarily be a washout. Could have plenty of sunshine with the usual risk of showers that come with warm humid weather.