Btw I was talking about the first one, the second one, if accompanied by a nice big collier can swaf about 850 missiles. So yeah I can see why you are having trouble.
Try exausting this defense, throw in heavily armoured missiles and the defenses should run out of missiles though.
I say if you get a nice supply of those missiles and you should be good to face about any missile onslaught the galaxy might throw at you.
Just keep a nice beam wall to catch any lucky bastards.
Also, 40000 km/s is already crazy good for your tech level, and unless the world has changed a lot in this game the AI sucks at point defense. Just dont get too cocky. Numbers can make a lot of diference