Is it permissible to blow into one's cupped hands, recite Al-Mu'awwidhatayn (Chapters 113 and 114 of the Qur'an) and Al-Ikhlas (Chapter 112), and then wipe with them over all children at once, or is it necessary to repeat that for each child three times?

It is permissible to recite the Mu'awwidhatayn (Surahs Al-Falaq and An-Nas) and blow into one's cupped hands, then wipe the child with them. The Prophet, peace and blessings be upon him, used to seek refuge with the Mu'awwidhatayn from jinn and the evil eye. It is reported that he would recite them, blow into his cupped hands, and wipe his body before sleeping. Aisha would do this for him when he fell ill. It is sunnah for the reciter to cup his hands together, recite, and blow into them, then wipe the child. It is safer for each child to have a specific ruqyah (exorcism/spiritual healing) and wiping dedicated to them.