In Japan child nudity is not an uncommon sight in fiction, simply because it's seen as a sign of innocence. It's stopped being as much of a thing in newer works because Japanese Media is nowadays made with US localization in mind because if your shit becomes popular in America, it's like getting a blank check.

It's actually why in the Japanese Version of Earthbound (Mother 2) Ness is naked in Magicant. (in the US Version he's in his Pajamas)