The idea of entire villages in Japan populated exclusively by futanari (a term originating from Japanese media for characters possessing both male and female sexual characteristics) is a purely fictional trope found in certain adult manga, anime, and online fantasy communities. No such communities exist in the real world.
In reality, intersex individuals—people born with variations in sex characteristics that do not fit typical binary notions of male or female bodies—make up a very small percentage of the population globally, including in Japan. They are not concentrated in any specific geographic location, nor do they form segregated settlements.
The "futanari village" concept is a creative invention for erotic or speculative storytelling and should not be mistaken for a sociological or demographic phenomenon.