From what I know from my buddies in the Marines, the Marine fighter jocks had to practice "dead stick" runs in case they lost their avionics and electric assisted controls. Now, since they were practicing for such instances, I think the military craft might be shielded a bit, but I don't think it's quite the "all impressive prevents any problems" sort of shielding. I think it might help on the outer fringes of the EMP burst or something, but anything caught well within the EMP burst is probably going to have some serious problems working.
For civilian stuff, you'd definitely have to be dealing with older vehicles and aircraft. Anything newer...new cars with their little "brain boxes" and chips, and new aircraft (as was mentioned with electric fuel injection) would have some serious problems. Unless a crafty mechanic can figure out how to bypass that stuff, the vehicles would be pretty much useless. Modern cars won't let themselves be started without their chips working.
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