The good news is that EMP has been a defense issue for many years--for as long as there have been nukes--and as far as I am aware, almost all military systems are shielded against it.

The main concern is civilian systems, which would make our economy possibly vulnerable even if our military wasn't. I don't know how much effort is made to shield things like, for example, banking computers or electrical substations. I wouldn't mind learning more about that myself. Automobiles would definitely be more vulnerable now than they were back in the old sparkplug/distributor days.

One bright spot is that the movement toward optical storage for data, which is not vulnerable to EMP, may mean that eventually at least much of our data would be safe.