The Fourth Commandment — in the context of the other commandments and, indeed, the whole Bible and the Catholic moral tradition — implies that to be honored parents must first of all be honorable and upstanding. There is nothing that states or implies that children must yield to and honor the behavior of parents who act dishonorably. Teachers and catechists must always make that point clear in an age-appropriate way.
Second, I would say that with the vastly improved identification and procedural systems in Church and society regarding child abuse, it is less likely that children will be misled by the Fourth Commandment. Balance, subtlety and wisdom in catechesis and in the general nurturing of children are the keys to avoiding problems here.