
I have often asked this question my self, but I think that the reason is two fold. First, the danger of having a weapon that could take out ALL electronic equipment in such a large area would be phenomenal. Remember that one of the ships was sabotaged in the second movie causing them to lose their ship early and cause the lose of their ship to the sentinels. What would have happened to zion if every electronic device could have been dropped early by sabotage? They would have been over run and killed without a fight.
Second, I think the sheer magnitude of creating something large enough to defend the entire city at every exit was simply beyond their technological capabilities. If it was plausible, they may have tried it, but thats a large under taking when you think you are safe well under ground.
You could have something similar to an electromagnetic grenade or charge that would be set off where you needed it to, in fact if you had enough of them in certain places then before the robots even reached Zion there would be one going off to stop them in their tracks.