Is it halal to learn Japanese as a hobby even if the county is atheist and has a history of idol worship?

All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.

Like any other language, it is permissible to learn Japanese, especially when there is a need to do so. Actually, there is no harm to the person in learning any language, and "learning languages" cannot be prohibited due to the disbelief of their native speakers. Permissibility is the original ruling for learning any language. On that, scholars believe that Allah, the Almighty, has taught Adam all languages.

Commenting on the Saying of Allah, the Exalted, {And He taught Adam the names - all of them} [Quran, 2:31], Al-Qurtubi said, “Adam (peace be upon him) is the first person to speak all languages – a fact recorded in the Saying of Allah, the Exalted, {And He taught Adam the names - all of them} [Quran, 2:31]. All languages are nothing but names, and thus they are included in these names. This is a point evidenced by the Prophetic Sunnah.”

Al-Baghawee, on his part, said, “Exegetes opine that Allah, the Exalted, taught Adam all languages and then each of his children spoke one particular language and dispersed into many lands.”

Allah knows the best.