What I did was to find a large shopping mall (usually either a dept store or Tokyu Hands or Yodobashi Camera store or BIC camera store) to spend a few hours shopping while the typhoon is supposed to go past the city I'm in. Then by the time I'm done with shopping, the typhoon will be over. That's what I did when I was at Kyoto on a typhoon day.
Try to come up with a few backup options in case of heavy rain/typhoon hitting some days of your trip. Indoor attractions, large shopping malls, and if trains are suspended, then maybe look up indoor attractions/shopping malls near your hotel so that the day won't be totally wasted.