The Metropolitan Opera, in an attempt to be innovative, presented a 90-minute, English language version of “Die Zauberfloete” geared toward children last season. But the Amato Opera has been doing this sort of thing for years. This weekend, that most imaginative of all audiences, an auditorium filled with children, had their first enraptured encounter with “The Magic Flute” at the opera house on the Bowery.