Too Late?
 

This is a question you should be able to answer easily by looking at one of the lodging booking engines, Booking.com or similar. As you get to mid-November, you are heading into koyo (fall colors) season, so lodging might be harder to come by then.

I wouldn't think so, unless you only want to stay in small, popular places (e.g. high end ryokans). Toyoko Inn, for instance, only releases its rooms for people who don't belong to its loyalty program three months out.

We often go to japan sometime from late September to early November. Air fares are usually very good, and it's easy to get hotels. August would be very early planning for me!.

Since your trip will continue into mid-November, you might want to book smaller towns or nice ryokans in the beginning of your trip and for the nights closer to mid November, visit cities like Kyoto or Tokyo that have lots of hotel options.

It is not too late and it is not too early - depending on where in Japan you are going. There will be a few extra visitors this year because of the Rugby World Cup, Sept 30 - Nov 2. Matches are held in different cities. You might be too late for reasonably priced lodging if you are visiting a city for the rugby.

I was planning an October trip and wanted to stay a night at the Marriott at Tokyo station on points but there was availability on just a few days in the middle of the month and not days that I wanted. There were plenty of dates available for a stay on points in November. A month ago the rate in JPY was something like 37,500 for Oct 25. It is now sold out. The rate for Nov 8 is just under 20,000.

If you are not there for then go were the rugby isn't. If you are there for the rugby then good luck.

It isn't necessary, given the JR network, to stay in a city where the Rugby WC or Olympics are held. I was at Nagoya station late one afternoon when I decided to go see a baseball game at Tokyo Dome and then return to Nagoya for the night. That was a bit wacky, but fun. A day trip to Tokyo would be easy from Nagoya, Matsumoto, Utsunomiya, or closer.

The forecast is for 400,000 foreign visitors to Japan for the Rugby World Cup. That is over a period of two months and a few days, but probably skewed towards the end of the tournament. There would also be Japanese traveling for the RWC.

Not too late at all. It depends a lot on where you plan to go of course, and hotels on Saturday nights can be much more expensive and harder to find. But it is not a peak period (though near the end you are hitting some of the autumn colors season). I didn't see anything in your post relating to rugby, and I don't know your planned destinations, so I can't say that is relevant.

Am in the middle of planning my October trip to Japan right now. It is absolutely not too late.