Yes. In fact, it is probably more important that the charger is in the bag than the ipad. Being an electrical engineer with considerable radio technology experience, I have a perspective that is a bit different than most on the subject. The true danger of EMP is in having antennas or things that act like antennas pick up the electrical energy. If the object in question either has wires or parts that could be considered long antennas or is connected to parts that could suffice as such, then the object is in danger of being susceptible to EMP. Many modern cars fall under this category because they are basically networked mini-computers with considerable wire interconnecting the various parts. Your iPad alone does not, unless you have it connected to the charger when the EMP hits. The charger (with cable) and house wiring that the charger is connected to becomes that antenna that makes it hazardous to your iPad. Unless you are at ground zero, or very close to it, your normal electronics won't have any problems surviving. The advantage to the EMP bag is that it will block any wifi or cellular signal and keep Alphabet agencies from activating the camera or microphone to spy on you. As for protection, the charger is probably more susceptible to EMP than the iPad, just because of the length of the cord attached to it. Most modern electronics are made from such sensitive electronics that they are designed with ESD/EMP protection from the start. The integrated circuit has built-in shorting diodes, and the circuit boards will often have additional protective circuitry. The manufacturers do not know where you will be taking your electronics, and the protection is cheap insurance for them. It is easy to protect objects that are not connected to anything from EMP, because the induced voltages will be so small. It is much harder to protect anything connected to the power lines, phones lines, or even many local computer LANs that have miles of unprotected cable.