That is what he wants you to think.
As far as radiation from the explosion, I don't think there is anyway for us to know that. For all we know, their ships had radation shielding of some sort.
And as for EMP, ZAFT stuff is equipped with things that cancel out the effects of EMP. Remmeber in Gundam Seed, when ZAFT attacked Panama, and detonated an EMP device? The ZAFT mobile suits were uneffected by it, while the Earth Forces who didn't have them equipped, got pwned.