1. Is airbus FBW susceptibility to damage from nuclear explosion electromagnetical impulse sign of bad design?
No - no airplane, civil or military, is designed or can be designed to take mayor nuclear trashing. FBW or othervise. Forget about Air Farce One being immune to nukes, it's only for the movie purpose.
2. But if we have manual reversion, we could still be able to land even with FBW burnt out.
Perhaps. I admit that I oversimplified things when stating that Airbus would spin out of the sky. You could eventually still control it via rudder and stab trim. But if you followed the link supplied by error_401 you'd find that if you're close enough to nuclear explosion to get your electronics damaged, you're also close enough to get lethal gamma rays burst. Actually now you have two options: getting killed in airplane crash or dying of radiation sickness couple of hours later. Besides, mutual-assured-destruction doctrine is still alive and there are hardly chances that first explosion wouldn't be followed by hundreds of others. Are you still sure you want to live to see next 30 minutes of world war 3?
3. Yeah but what with directed energy weapons? You just keep telling me about nukes.
DEWs are sci-fi and speculational weapons. When (and big if) they are fielded, they won't be there to damage your electronics. If anything like YAL-1 or MIRACL is fielded, it will be able to drill nice hole all through the airframe and everything within it. Wikipedia has nice article about limitations of (once again: hypothetical) DEWs. I guess this answers "What if DEWs fall into hands of the terrorists?" question also.
4. With 10000 hrs over 20 years I could land B737 in manual reversion.
Well, with one 737 sim session that covers manual reversion you would have known that this isn't joking matter. Oh and you've just had your electronics fried by NEMP, remember? No IRS, no EFIS and no FADEC too. If you're flying older 737, there still might be functioning standby airspeed indicator, standby altimeter and perchance standby horizon too, but with new maschine you would be limited to looking out the window. Now if all you see is inside of the cloud, dismissal comes pronto. In VMC you can extend the agony but not by much.
5. By the way some civilian aircraft do have ECM pods.
Yes they do, and they are there to thwart the radars - that is to prevent search radar from finding you, targeting radar from acquiring you and missile radar from guiding the missile towards you. And there El-Al planes equipped with IR flares dispenser to spoof IR guided manpads. ECM are not there to create the protective cloak wich shields from NEMP or DEW.
6. I simply cannot go back with a load of reasons why the question should not be asked.
Questions were asked and questions were answered. Now go and tell your editor that you have no story.