Here's the sad news. We can't stop weapons from coming into this country. If we could stop a bomb we could also stop all drugs from coming into the country. Do you think that's possible? I don't believe we could stop all drugs from coming into LA, no less the whole country. If fact, since we have drug sniffing dogs, it's more likely we could stop all drugs before we could stop all weapons.
This isn't a little country like Israel. It's not small, it wasn't developed with enemies on all sides.
The sad truth is that defensive stances won't work. And that leaves the other, not as comfortable choices. One is MAD. Mutually Assured Destruction. It worked for many years with the old USSR - and it might work with the Arabs. We're limited to some extent with Arabs - we don't "get" them. That's a big problem. We always understood the Russians - they were chess players. And their leaders were goons. Typical totalitarians. AQ is that, but more. There's a "true believer" element in them that's unstable. And followers who are both zealots, unsophisticated, angry, and enthralled with cult charm. Not a great mix.
This is a very bad situation. Add into it that our real enemies (like North Korea) could arm AQ and wipe out two or more groups they could do without).
As to EMP's the best way around them is find cheap ways to start hardening our chips. It would be too costly to redo the ones in place, but there must be some stop gap measures that would work for some. Then replace them on a priority basis -- most crucial to keep the society running first. Power plants, grids, etc., are first. This war isn't easy. Lots of pitfalls.
EMP's will take an air burst. Unless the islamokazis develop , or buy, their own ballistic missile the point is mute.