well, i'm sure that when a nuke got dropped in a particular area, any machine in that area was destroyed regardless of emp emissions (we're talking strictly the force of the blast here). maybe what they meant when they said that the machines were not harmed by the radiation is that no outlying machines outside of the blast area suffered anything like cancer or bubbling internal organs from the heat. i'm sure the nukes were effective to a degree, just not as much of a kick as if they were used against humans.
but i've got no answer for the emp thing.