Ya think humans, as smart as they are, would have known to detonate the nukes at the appropriate altitude? Seeing as that quote comes from umm... common human knowledge? =)
Either way, if the machines could have figured out a way to defeat lightning, then they should have figured out a way to defeat the lightning guns the zionists were using against them.
-Al
I highly doubt that if they were stupid enough to block out the sun, they would even consider EMP. In the Animatrix(or whenever we tried to nuke em), they were obviously hoping that the heat/radiation would kick the machines' asses. After that, I don't think they had a chance to retaliate.
Perhaps the machines lied, but I don't think so. That's the beauty of Machines; they can turn it off. Plus, I think that many of the assorted AI programs are starting to get really sick of the war and really don't want to continue.