Since your microwave can keep the energy it generates within it's three walls and a viewing porthole, it will do the same and keep anything inside of it (your cell phone, iPad) safe from the energy dispersed in an electromagnetic pulse.
The walls of the microwave are made of conductive metal, with the viewing hole similar to a mesh wall in a Faraday cage, making a microwave a hybrid Faraday cage. I measured the holes on my microwave and they come out to 1 milimeter; small enough to theoretically block a pulse with a frequency of up to 300 GHz. An electromagnetic pulse would give off energy with a variety of frequencies, but your microwave should block the bulk of them.You can test your microwave by placing a radio or cell phone inside of a microwave (don't turn it on!) and checking for signal. Can you call the phone in the microwave? How is your radio reception once inside?
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