Worms wont cause mishapen eggs as far as I know and they are too young to molt. The sneezing could possibly be caused by their feed (dust particles) or pollen in the air, maybe from their coop...just might need cleaning out. Put your ear up to their breast, do you hear any gurgliing, wheezing, rattling? If you do, it possibly could be a respiratory issue. If it causes mishapen eggs in conjunction with a respiratory issue...I'd suspect Infectious Bronchitis (IBV) which is a viral disease and contageous. Since it's a virus, antibiotics are useless. If this is what they have, this would be why there's a slow down in egg production, eggs will become wrinkled and the whites will be watery-like. In time, the effects of the virus will go away but they will remain carriers and egg production will pick up but at a slower rate, the eggs will look normal again, maybe an occasional wrinkled egg. The eggs are safe to eat wrinkled or not. Your flock will have to become a closed flock...none in,none out. If it was only one hen giving you a mishapen egg, it would probably be nothing at all, an anomaly or maybe an issue with the reproductive system...but with half your eggs turning up with the 'bump' in the middle can be an issue.
Another possibility is if you added or deleted something in/from their diet? Try giving them some scrambled eggs in their feed and see if there's an improvement in egg quality. Good luck.