I have a feeling it's glitched for me. I tried about 10 times with a live coop friend (we had gone through hard together) and it wouldn't unlock. Then I went through the entire coop campaign again with an offline GT, loaded up Zone 6, went all the way through and destroyed all the ships, and it still didn't unlock. I loaded up Zone 6 again, went through it again and destroyed all the ships, and again it didn't unlock. The writing it on the wall for me with this one I'm afraid
Edit: It just unlocked for me. Local didn't work and my online coop partner decided we should try it again. We went through the Zone like normal, nuked every ship in area 29 (including the big one half way through) then got about two thirds of the way through area 30 and it unlocked for us. Meanwhile, there were still ships that we hadn't even run into yet, but I'll definitely take the achievement unlocking early rather than not at all. What a goddamn glitchfest of a game.