Natural disasters (check out details, please)

I'll be traveling to Tokyo > Kanazawa > Kyoto (between 19/09 - 04/10). Should I avoid some of these area(s) due to an increased risk of natural disasters? Thank you.

You can�ft predict earthquakes and tsunamis with the kind of accuracy that you are asking for. Typhoons are different, but most of the effects won�ft be known until after the fact. Just stick to your plan.

In what way has the risk of natural disasters �gincreased?�h

Risks are everywhere, not just in Japan. Even if you stay home and never go out, an airplane can crash into your house. I do remember worrying about earthquakes before my first trip to Japan, but you cannot live a life worrying about all possible things that could go wrong - life is too short for that. I have been to Japan 3 times now, and planning for the 4th. I did experience an earthquake once there, fortunately there were no damage where I was at the time. You should check to make sure all the trains you plan to take were not affected by recent events.

Might the OP be asking whether there is an increased risk of landslides in the area she is going with the flooding and earthquakes?

There is no increased risk, and the places you are going are largely unaffected by the recent storms.

answer is simple yes there are always risks even if you leave your home.

Natural disasters can not predict only "Earthquakes".
Earthquakes occur somewhere in Japan every day,
but the same as a traffic accident no one knows the outcome "how bad or not".
Only In 2011 when "Great East Japan Earthquake(3.11)" occurred, 300,000 earthquakes were observed,
among them, the number of sensuous earthquakes (level 1 and higher) exceeds 10,000.

This is last year 2017 "traffic accident" record in Japan as sample of comparing.
Number of traffic accidents : 472,069
Number of injured persons : 579,746 (including passengers, walkers and more)
Died who within 24 hrs(1 day) : 3,694

If still wondering you should read JMA web all.
https://www.jma.go.jp/jma/indexe.html

It will not be like this movie.
https://www.imdb.com/title/tt1190080/

earthquake: unpredictable.
typhoon: that time is typhoon season. possible from Okinawa to Nagoya, Shizuoka (maybe rare to Tokyo). so, Shinkansen might be stopped.
if you encounter a typhoon, you can't do anything in one or two full days. they will restart public transportation after they confirm they are safe.