All of my children have used clipless pedals on our tandem from the outset. We used the small size 34 shoes mentioned above at first; the middle child now fits 35s and the oldest has since graduated to size 36. There she might stay, as her mother takes size 36 as well; they share the same pair of shoes now.
As we ride a da Vinci with their unique Independent Coasting System, we don't have to worry about the stoker cranks spinning around and slapping unsuspecting young legs, but I feel having them as fixed to the bike as possible is the safer route. For the first few rides with each child, I needed to clip them in by hand even though the tension on the pedals was a low as possible. They all quickly learned the knack and can clip in alone now.
Even my wife, who will not ride clipless pedals on her single sings their praises on the tandem.