IT depends on the strength of the emp wave. A government study showed that some cars might be affected but not all during a moderate emp blast. What will be effected are complex electronics like cell phones and computers. If the car is computer controlled chances are it will be effected.
The only way to be certain that your electronics will not be permanently cooked is to construct a Faraday cage around them however in a moderate to heavy blast the pulse will propagate through the power lines and blow anything that is plugged in.
The kind of thing you are worrying about is a kind of doomsday scenario.

I'd say if this happens we will all have a whole lot more to worry about than will MY car start, there are increasing catastrophes happening globally and the more these things happen the absolutely More are our resources (meaning here; charities and all of the countries that usually rally to aid) are being depleted. So I would urge you to research all that you can do for individual emergency Preparedness, starting with considering each Type of possible crisis that Could occur where you reside. and then start prepping. just consider this, it's good common sense-don't be a proverbial ostrich.