Think again propeller head. ;)
The EMP is more a fundamental effect of the detonation, not the atmosphere. A burst in the atmosphere is modified as most of the thermal x-rays (most of the emitted energy) are absorbed in the very-nearby atmosphere while the fireball radiates sucessfully in the IR and visible, cooking the shiznit out of the surroundings.
Check this out if you don't believe me. Under real EMP weapons.
http://www.fas.org/irp/agency/army/tradoc/usaic/mipb/1997-1/merkle.htm