True, the OP mentioned spent fuel. I also don't see EMP and spent fuel being such a bad combo. Spent fuel is still "hot"--radioactivity and heat-wise--but it's no longer capable of sustained fission so it's not going to blow up and spew radioactive fallout or anything like that.

Without pumps, it could boil off the water in the containment pools, but I don't believe they are hot enough--temperature-wise--to cause any sort of China Syndrome type of event by melting through the floor of containment. Still, definitely not good being inside the containment building with bare, exposed spent fuel around due to the radioactivity.