http://www.geocities.com/CapeCanaveral/5971/emp.html
Lightning is charge transfer that occurs in a localized "ion channel"; and, this propagates kind of slowly. EMP is more like a wall of high energy photons. These photons are emitted from charged particles that gained thier energy from an intense gamma ray burst. Lightning arrives in a stream. EMP gets you all at once.
My point is that EMP is EMP no matter if it is created by nuclear blast or lightning.
If it's lighting caused EMP you're worried about, you needn't worry.
If it's the nuclear bomb EMP you're worried about, you should worry about the nuclear bomb, not the EMP.