However Fly by wire systems have multiple electronic redundancy systems, and if all fails the controls shift to direct mechanical/hydraulic actuation which is a standard contingency feature. However remember that relaxed static stability/ FBY aircraft are computer controlled and the controlled surfaces are constantly manipulated for controlled flight. If the system were to fail, even if hydraulic controls are available , controlling the aircraft would be very difficult to say the least. But stil, with regards to your question, all FBY aircraft have direct hydraulic/mechanical actuation systems in case of FCS failure.
this is the point. modern aircraft's maneuverability is primarily based on controlling a number of control surfaces, which are generally controlled by sophisticated algorithms (like gain scheduling, LQG, Kalman filters), which in turn are processed by flight control computers, which are at this point at best rad-hard microprocessors, which are no match to an EMP weapon which is specifically designed to produce very large power pulses (GW range), in this particular event you have at-best, a manually controlled (lot of reduced maneuverability) aircraft. Now either the flight control computers are EMP-hard, or you have a pilot manually flying an un-stable machine.
so it *might* make sense to review the whole design / specification process (not only of the electronics, but the control surfaces also) until or unless you have a proven EMP-hard FCS.