I do find that if my air cells are underdeveloped, I get a lower hatch rate. However, the others are correct that eggs are hardy and most should still make it. With well-developed cells, I generally get an 85-90% hatch rate. With underdeveloped, that drops to around 75-80%
People are going to start thinking of me as the "dry hatch preacher" if I'm not careful, but the truth of the matter is that nothing has improved my hatching success so much as running dry hatches has. On those occasions when I've had to run a higher average humidity (for instance, when I had other eggs hatching in the same incubator and had to lock them down with eggs that were not ready to hatch) and ended up with smaller air cells, more of my babies died after pipping.
It is sad, and I always feel bad about it. But nature doesn't always provide perfect conditions either--I have a broody (duck) hen whose eggs I had to replace because she decided to nest outdoors and it rained for three straight days and the eggs spoiled. So don't feel too bad. You'll probably still have a really good hatch, and you now can adjust your humidity practices and see how it affects your next hatch.
There's probably not a lot you can do, but there are two things I would do in your situation. First of all, I would remove all humidity sources from the incubator until lockdown. Then, I would not lock down until I see one or more of the eggs has internally pipped. If you do this, you'll want to check the eggs a few times a day with a good strong light to look for internal pips. If you're not sure what to look for, you might want to ignore that particular advice--it's just what I would do, but I'm very confident in my ability to tell when an egg has pipped internally. It would give the eggs slightly more time to dehydrate without letting them shrink wrap (that danger begins after the first *external* pip occurs), but if you miss one and it pips externally before you lock down then it could end up shrink wrapped.
Secondly, I would hatch them on their sides rather than in a carton (which you may have been planning anyway). I usually do hatch upright in cartons, but I have this idea (based on observation and reasoning, but untested so it's not technically a theory) that when a baby has a smaller air cell, it has to work harder to keep its little nose above the liquid inside the membrane and is more likely to drown. If it's in a carton, it has to work against gravity to keep its nose up, but on its side it might have an easier time.
Like I said, that's just what I would do. I don't know whether it would actually help or not, but it makes sense to me and might be worth a try. It's unlikely to hurt anything, anyway.
Good luck. I bet you'll have a great hatch. I'm on Hatch Number 11 (for a total of about 150 babies) and every single time I get worried about SOMETHING that is different or "wrong" this time around. And so far, every single time I've had a decent or excellent hatch (never below 60% anyway).
Enjoy!
