EM and EMP are different. EMP, the Electromagnetic PULSE, is what you're probably thinking of when you talk about disabling drones and electronics. It's a very specific kind of effect, and is the EM equivalent of an explosion shockwave. EM weapons can deal anything from cancer causing gamma radiation, to flesh searing microwave radiation, and all manner of in between and around. Take a look at any of the laser crystals. ALL of them are based somewhere on the Electromagnetic (EM) spectrum, but none of them constitute an EMP.
Similarly, all of them will probably make jelly out of crewmembers, but not all of them will have an effect on sensitive electronics beyond thermal damage.
I would wager though that the missiles and projectile shells DO deal in EMP, instead of directed EM radiation, so those would be a significant thread to electronics.
Just because you're using EM (read: Electromagnetic) weaponry doesn't mean it will disable electronics, and it certainly doesn't mean fleshy crews will go unaffected.