Well I'm no expert but of course there will be a lot of redundancy in the systems, ie multiple computers and circuit paths, including power generation to ensure the probability of a complete failure is extremely remote. I fly a helicopter that requires hydraulic flight control boost - its unflyable without it so if I suffer a double hydraulic failure I'm gonna die. However there is a lot of isolation and 3 pumps to help that not happen.
Core systems like that are protected from lightning effects even if some of the less critical peripherals aren't.
Nevertheless I'm sure that certifying the first civil FBW helicopter will be challenging!
Modern military aircraft have EMP shielding though I suspect it depends on how close / the magnitude of the EMP.