I have recently encountered a website - offering free and commercial services - which belongs to a company located in Japan. Although the service is, what I believe, quite popular, the ToS are available in Japanese and English, whereas the English version is poorly translated and some of the points are rather ambiguous after translation, some even unreadable. Shouldn't the company be obliged to share properly prepared ToS? Moreover, if I accept the terms, am I obliged to comply with all of them, or rather only the understable points?
You are obliged to abide by the terms that you accepted. When you click "agree", that is whatever terms are offered in that box, or in the link contained in the box. That could be the Japanese version, or the English version, it depends on the circumstances. This assumes that you didn't run a fully-Japanese page through Google Translate. The writer of the contract bears responsibility for any errors of translation, including the writing of complete gibberish. However, if a dispute is litigated in Japanese courts, the common law doctrine contra proferentem doesn't exist per se.
You are obliged to comply with the Japanese terms
Unless a contract provides that a translation is definitive, it isn’t - it’s simply a courtesy. For a Japanese company under Japanese law the Japanese terms will be definitive.
Depending on the nature of the transaction, if the English translation is so poor that it amounts to deceptive and misleading conduct under applicable consumer law, this may modify the contract or allow you to void it or give you additional rights outside the contract.