I don't really know. We know that highly ionized particles can penetrate an ISDs shielding and render it all but useless. And Star Wars has featured EMP before, but mainly against small, relatively unshielded targets like droids or fighters. Against a capital ship, if the blast is big enough, I think it would go through. But as far as I know, humanity has yet to develop something so miraculous, the exception being nuclear warheads, but again...