An EMP that would knock out a robot plane's computer would also knock out a manned plane's computer. Since all the new designs are fly-by-wire, and are unstable without a computer continually tweaking the flaps, the human pilot would be in real trouble
That's why modern planes' electronics are heavily shielded against EMP
A bigger concern would be an enemy cracking the encryption for the command channel. Suddenly, his hackers make all your bombers, THEIR bombers
Or, as the orientals like to say it: "All your base are belong to us!"