The Templars apprentices arent, they join the order at young age. So you are condemming them to muder/enslavement when you side with the mages.
There is no mention at all in DA:I of templars having children at Therinfal, but Fiona flat out states during a dialogue with Alexius that there are children among the mages. I presume children templar recruits were sent to the chantry, or dead in the fighting that occurs during the pre-game events. I can't see Knight Captain Whosit letting any of the kids live once he started corrupting the order even if they had gone to Therinfal. They wouldn't withstand the red lyrium ravaging their bodies, and they lack fighting skills, since Alistair will tell you in Origins that the fight training doesn't come till 'later' when they have the physical stamina/strength to learn.
I'm pretty confident that any kids among their numbers were elsewhere away from the fighting or already dead.
Mage children, however would be just as powerful as their adult contemporaries and potentially useful as slaves/cannon fodder.