As soon as the magnatron powers up, the CD is stuffed. Wheres my reference? My kitchen and some of my friends kitchens. Ive put cd's that dont look damaged back into drives to try and read them. Feel free to come around and test. You dont need the 8 seconds. The 8 seconds was to let people know that it might get a little dangerous and that they look pretty cool after a few seconds.
The microwave is a high frequency eletro magnetic wave, an EMP is a electr magnetic pulse. Both will induce electical currents and not just in a wire conductor. In what way do you not think that a cd will not have any induced currents.

As to how much damage a device will make depends on its design, size, location etc and how many of them there are.
As to the likely chance of this happening, I think I will be pretty safe where I am.
I am more worried about lighning around here, as this is a much greater risk. Protecting for lightning will provide some protection from a non nuclear EMP if the device doesnt go off close.

Some of the damage Ive seen caused by lightning has been a 1 inch bolt holding a plate on a wall blow itself apart and embed itself in a limestone wall on the other side of the room.
Ive also seen a builbing take a hit through an antenna on the roof which looked like an afro. Every computer in the 3 story building had its BIOS ROM chips wiped, even the ones not switched on.