Professor Quantum knows about the kids' time-travelling to Bible times.
The series' website says Professor Quantum built Gizmo to be Chris and Joy's companion and protector. Gizmo has a whole plethora of gadgets built into himself that help the kids to navigate their way around Bible times, including a geo-sensor that identifies the year and location where Superbook takes them on a given adventure. The only way Gizmo could have things like that built in is if Professor Quantum knew to put them there; and by extension, the only way he would know to design those things is if he knew the kids would be time-travelling to Bible times. Which therefore means he must know about Superbook, but is being a Secret Secret-Keeper