This is a really interesting question, imho... though you may want ask the derisive engineers you mentioned if they know something you don't before pursuing further!
I don't consider myself terribly familiar with the mechanics of an atmospheric EMP attack... but let me try to describe what I've heard of and what I would do to safeguard against one. Let me know if we're talking about the same thing.
So basically, an EMP attack would involve someone launching a nuclear warhead way high up into the ionosphere, and detonating it. If done properly, the theory goes that the ions floating in the atmosphere that high up would react to this blast by being forced downwards very quickly, creating a rush blanket of charged ions across, presumably, an area as large as the United States.
This rush of ions, flying through most materials (concrete/metal/people) would not harm us as organic creatures, but would induce wildly high and erratic currents in power grids, communications grids, and any electronic devices large and small. On a large scale, power plant generators will explode creating a massive blackout as our power grid becomes useless. On a smaller scale, all cell phones, HVAC/refrigeration equipment, computers, and most vehicles will be rendered partially to completely useless.
What seems evident from this, is that if it's even possible to provide EMP blast protection shielding within the customer's systems, you'll still need to at the minimum isolate any of the customer's communications and power from the grid... On the other hand I thought I had read that an EMP blast would go through nearly everything, including typical "metal cage" shielding as is featured within most PC cases... perhaps something more substantial, like lead panels, might redirect a charge blast of this magnitude?
I'll be watching this thread with interest =).
