“Honor thy father and mother” is numbered as the fourth commandment in Luther’s Catechisms. It remains the fourth commandment in Lutheranism.
While Luther’s catechisms were certainly not the first Christian catechisms, they were the first of the “simple definition” style, and actually served as the model for the Roman Catholic Catechisms that would come out of the Counter-Reformation. Prior to this, the numbering of the Decalogue was somewhat arbitrary; it was not uncommon for Catholics to number them differently depending on their local tradition. So what you consider the “Protestant” numbering is, in fact, quite acceptable.