Yes, it can fry the components inside the engine causing major damage. Or it could even damage the ones that connect the engine. If you feel that this has happen you should take it to an auto mechanic and have him check it out to see just how much damage has occurred.
Yes, lightning can fry components inside the engine or that connect to the engine. You should open your hood and examine your car, and if you can't remedy the problem, then you should have your car fully examined by a mechanic.