https://youtu.be/OzV1GlDDlv8?t=2m1s the prydwen gets destroyed, presumably in one of endings where you side against the brotherhood. But In game I saw BoS squires on board. And obviously you are not allowed harm children in Bethesda games. So put two and two together, how do they survive?

They die "off screen" along with the rest. The same thing happens if you destroy the Institute (there are children there too). You may not be allowed to blow a kid's head off, but nuking them is a-ok.

Darn, I was hoping for immortal prepubascents to walk out of the burning wreckage terminator style, thirsty to avenge their deceased parents.

They survive Fatman rounds, they will survive a blimp crash. Unless you got a killable children mod than you can shoot them if you want.

Yes, same with Megaton in FO3.

some settlements in FO4 also have kids no idea that happens if they are attacked while you are away.

I actually used the evacuation order so all non-hostile personnel in the institute escaped the blast.

I think the real question is WHY THE #!;$ ARE THEIR CHILDREN ABROAD A WARSHIP IN A DANGEROUS MILITARY EXPEDITION?

Well that, and also, we have asked the players not discuss child-killing or lack thereof in the games on the boards -the threads tend to get ugly and require too much babysitting.