Small Soldiers/WMG

The chips being EMP-sensitive was not the real main reason the military didn't adopt the X1000
The real main reason was that someone in the military realized that giving military equipment intelligence and the ability to learn isn't all that good an idea. The reason they didn't tell the designer that is that they didn't want to offend the genius capable to making chips with those capabilities by rightly implying he was a moron for not realizing that himself. It not being all that cost-effective to give something that will be used for significantly less than a day (any single missile) the ability to learn might have contributed, as well.
 * Of course, given the way that the toys reacted to having the chip installed, that is the shift to the extremeness of what was originally reasonable personalities ('Defend Humanity at all costs!' and 'Learn about this strange new world!'), we could assume that any missile with the basic instructions of 'Be fired, fly through air, destroy the target' would become a zealous engine of destruction for it's singular purpose. Whether that is a good thing, however, is still up for debate...