I've also noticed that some Japanese (out of 1000 maybe) had darker skin, almost like Indonesians (but they were pure Japanese, I am sure). Could they be descendant from the Jomon-jin who mixed with Yayoi-jin in Honshu, Kyushuu and Shikoku ?

What about Burakumin ? Do they have particular physical features ? How did people recognise them ?

In Edo-jidai, the Japanese class system was very similar to the Indian Caste system. In either country, there were 4 fixed classes (people cannot change class) + outclassed : the "Untouchables" in India and the "Burakumin" in Japan. Both were given dirty jobs and only them were allowed to kill animals and make leather.

In India, the caste system was established by (white) Aryan invaders around 2000BC to sepate dark-skinned native Dravidians and the new white-skinned ruling class (2 higher castes of priest and warriors). Obviously there has been some mixed blood since then, but generally upper-caste have fairer skin (sometimes blue-grey eyes) and lower castes and especially untouchables are darker.

Could the same have happen in Japan with Jomon-jin ? Are they the burakumin ? Do burakumin have darker skin ?