Mmm... yeeess... Sorta-kinda... I am not sure how easy it is to harden a missile against EMP counter-measures, but I suspect it might be a routine part of nuke design.  Remember that nukes seemed likely to arrive in large numbers in the cold war anyway. Maybe not now of course. Now, if you are about to level a country with nuclear carpet bombing, then it would be a shame if all but your first couple of bombs were useless because the subsequent lot were put out of commission by your own EMPs.

OTOH if you had to send your bombs in one at a time, that would be a real nuisance, making for n unacceptably slow and tedious war, wouldn't it? So for my money, Either EMP-hardening or impossibly precise synchronisation of your blasts would be necessary.

Conversely, if you wanted to intercept nuke missiles with other nuclear bombs, they would have to be clean enough not to poison your own country, small enough not to scorch your own country, and well-enough aimed to fry incoming, without wasting ordinance on decoys. Not easy.

Or you could send up electronic, conventional-explosive EMP weapons. I don't know how well they compare with nukes in cost, range, and effect, but although they would not strew radioactivity round the country, they too would present hazards to one's own side as well as the incoming, and the two effects would want some balancing.

As I see it anyway.

at john: for regular nuclear carpet bombing  it would likely, not be necessary to shield missiles to protect them as low altitude explosions do  not create a far ranging emp, due to the fact  that the emp is created as a reaction to the earth's  magnetic field, also the effects of  detonating  a few nuclear explosions  high above the ocean  to counter hundreds if not thousand at ground level   could be considered a necessary risk as some electronic infrastructure could be spared allowing a possible rebuild. (and would result in a substantial reduction in direct deaths)

 the point about shielding is interesting nonetheless, though i ask would it not have to be grounded to provide adequate protection

 sorry for typing this. my mistake

Rockets and nuclear warheads are encased in metal totally.

This is a perfect shield against  EMP.

Grounding is not necessary of course, such ideas 

are tyical for lack of understanding in electric basics.

Georg