Dunno, seems to me that lethal weaponry is already disabling UFO systems by overloading its power sources - else "crashed" ufos would look like so much debris strewn across miles. EMP weapons would work similarly. Also there is no evidence whatsoever that alien tech would be in any way susceptible to EMP, at least, not more than to any other form of energy. UFOs have very few moving parts and their computers have to work in different ways than ours - we read about "optical processors" whatever they are. But even leaving all that aside, since Alien Alloys are said to be superconductive, this amounts to UFO's hull being a huge Faraday's cage, which would naturally make it extremely resistant to EMP attacks.