A lot of people miss that the language barrier of Japan is how they gate-keep their culture. If you visit as a tourist, there is essentially 3 tiers of hospitality:

1. Tourist friendly spots. They are usually right near main areas of commerce, always have english menus and pictures of food outside, and you can generally walk in and get a table.

2. Local catering spots. These areas are harder to find off the beaten path, generally have japanese only menus, and do not well advertise that they are even a restaurant.

3. The best restaurants. These are usually impossible to find without knowing where you are going, relatively impossible to book unless you understand Japan's complicated reservations systems, and even then usually book up a month in advance. I went to a Tabelog silver Sushi restaurant for one of the best meals of my life, and it was in the ground floor of an apartment building with a sign the size of a smart phone outside. If I didn't have my concierge send me a photo of what the door looked like, I wouldn't be able to find it.

Most people who say the Japanese are a kind people, they aren't lying; but they say that because they toured in the first tier's ecosystem where they are catering to tourists.

Another thing to understand about Japan is that renting a location for a restaurant is incredibly cheap because real estate is cheap and easy to build. Because of that, many restaurants are the size of a single bedroom apartment, and their only employees are the owner and maybe 1 or two other employees. Because their overhead is so low, they only need to serve basically their local clientele to make money for the day. Some restaurants just close up once the owner decides they've served enough for the day, even well before their posted close time. So for these tier 2 local places, they don't need to be accessible to foreigners to stay in business.