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!"
Besides being unlikely, it would merely allow two different sets of commands to go to the craft (i.e. the U.S. and the enemy's commands). That would be a far cry from making the bomber all "theirs."
And on mission runs like today's...where the UCAV was pre-programmed on the ground for its strike, there doesn't have to even be a command line open.