He was able to capture David from a fortress full of heavly armored swordsmen and extremely power psy warriors.
I don't think that's right: he was able to capture David in a village that was not protected by any powerful Psy whatsoever, as evidenced by Uncle Flastaff telling the Main that only David could see the Shadowlings- meaning that even if there were any more Psys in the village, they were too weak to break through the Shadowlings' obfuscation.
He did not capture David from the Psy Academy. Tastidian, on the other hand, managed to do just that.
Anyhow, Noctus may have underestimated the Main, but the Main was such a valuable find to the Queen that I think she just might've allowed Noctus to be revived and to use his experience to do less important tasks (if he failed once,he may fail again, so he has to start with something simpler).