MikeNificent
Space Marshal
Microelectronics are the biggest weakness. Even the tiny wires in your mobiglass would likely burn up, unless they were shielded.So if we were working with real life dynamics the ship using an EMP would need to be 120% shielded, even the smallest gap in its shielding would render it useless - the EMP generator could even take itself out, i assume?
An EMP in space would be interesting anyway. Without an electron field (like an atmosphere) filled with electrons to push with an explosion in order to bombard surrounding ships with, it would be more like an MP. An MP would still induce current in circuits, would be tougher to shield against, and would also be tougher to generate without damaging your own ship.
Anyway, I'm rambling. The short answer is @Shadow Reaper is correct in that the computers would be the most vulnerable part of the ship.