Will’s middle name is Owen. It was his mother’s maiden name. It’s a nod to his Welsh heritage, too, if you know who Owain Glyndŵr was.
Welsh was heavily suppressed by the English during the earlier Victorian era. Will’s family would probably only have spoken it at home. This would have annoyed his mother so giving her son a Welsh middle name would have been a minor act of rebellion. If you want to yell at Will in Welsh, his Welsh name is Gwilym Owain Herondale.
Jem doesn’t have a middle name. Not everyone did in the 1800’s anyway. He has a Chinese name if you really want a three-worder: Ke Jian Ming.