I have never encountered this in other travels, and think I have been patted down by females (I am male), though maybe I am misremembering. Is the rule that in Germany (or the EU?) that nobody can pat someone down unless they are of the same gender, or that people being patted down have the right to ask for a same-gender person to do the pat down? Maybe that is a worldwide rule and I've never noticed. It seems a silly and backward rule for numerous reasons.
There was more than one woman working in the 'ladies only' line, but maybe only one was qualified to do the pat downs.