"Is Japan an intellectual country?" Interesting question. As far as I am concerned I would answer this question with a simple "no". This is however not limited to Japan. In my humble opinion no country can claim to be an "intellectual" country. Individuals are intellectual. Of course not all people are intellectual or even smart, that is (in fact most are not.)

My question is, why a country like Japan, that has an age-old reputation for the organisation of its society, refined customs and high literacy, didn't manage to develop more sophisticated technologies. Why does it take a single Englishman (William Adams), 400 years ago, to teach them about geography, navigation, building of ocean-faring ships, artillery, etc., which the Japanese learned quickly to copy, but never thought about themselves ? Why are all significant inventions until the late 20th-century concentrated in a few Western countries, and that Japan, China, and most of the rest of the world almost didn't contribute to anything to modern society ?
Before I comment on the actual content of your qoute, I have to point out that it seems that you are implying that Japan, or the rest of the world, is somehow inferior to the West. This said I personally do not believe that you did so on purpose, mind you. However your words can easily be understood that way.

To answer your question, why Japan did not come up with significant inventions until the late 20th-century: You have to consider quite a lot of aspects to answer this.

First, you mentioned it yourself, the way Japanese society is organized. As it looks like the Japanese mentality stresses harmony over individuality, thus reducing the amount of groundbreaking inventions or discoveries by brillant individuals (Nobel, Einstein, Darwin...[for the purpose of this reply I am only taking 18th/19th century scientists in account]).

Second, isolation. Unlike the West Japan remained isolated for a very long time. Europe has many cultures and languages, all struggeling for power. In order to survive or in order to remain dominant these nations had to change and to adapt.

Third, religion and cultural heritage. Concerning the West: Christianity, like all other monotheistic religions tends to be rather... how shall I put it?... violent. This is due to the fact that other Gods cannot be tolerated by the very premise of this believe system. Therefore strict rules and dogmata occur and all other forms of exegesis are branded as heresy. This is, of course, very oppressive, and will inevitably lead to resistance. This resistence was supported by the cultural heritage of the hellenistic era and it's subsequent philosophies. In Japan there was no such thing. Only Shintoism and Buddhism as religion and maybe Confucianism as philosophy, not enough to spark a revolution against the Tenno like against the French king during the French Revolution... (I do not know that much about East Asian philosophy though, I might be wrong.)

Fourth, luck. Plain luck. Because of the Industrialization the living conditions in Europe changed dramatically. This led to social unrest and new social classes, new social and economic structures. All of these in turn led to new inventions and discoveries. Europe was simply lucky to invent the steam engine first.

I guess the geography plays in as well. Of course all of these factors overlap significantly and there are countless other points one has to take into account (and I guess I was rather shallow in my analysis, but further elaboration is not necassary.). Everything I have stated here has to be taken with a grain of salt, as I am no sociologist. But maybe it is at least somewhat plausible.

By the way, how exactly do define "intellectual". Do you consider artists intellectual? Social scientists? Natural scientists? Knowledgable people?