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The origin of this custom is Byzantine (Orthodox)
Up to the advent of Protestantism, Christianity regarded God as the ultimate king. This is also the origin of the old Greek name for a church building: βασιλική (basilike, "royal"). In the construction of such a church, the throne & altar would be as far as possible from the door, against the wall (to protect the king from assassination attempts). This and the form & clothing of church ceremonies are taken from the prevailing customs of the Byzantine court. The same goes for the depictions of the Nazarene as a child.
The best known example of royal children depicted with crowns in Byzantine art is princess Anna Komnene.
Even after the schism between the Catholic and Orthodox churches, the depiction style remains prevalent in Western European art until the advent of Protestantism.