one big weakness with emp missles is, they have to be launced at space ports, and space ports blow up
people normally build spaceports right next to eachother so they can launch faster, but that also means that if you can get one supernova or 3 starflairs through, you can knock out their missle production instantly (and mabe blow up another critical building if they build haphazzordly)
just attack with a medium sized force of lynx, they would launch the emps but wouldnt get all the lynx, so they would send their defence to mop up, while doing that send in another wave of lynx so they send in a few more emps, if your lucky they would also emp their own units
while all this is happoning sneak a few starflairs or supernovas into their base for a nasty suprise