There are many, many hatching eggs shipped every year, and very few eggs - shipped or not - that develop neural tube defects. Something that specific in a group of eggs from one source would be more likely be due to a factor unique to those eggs that does not affect all the other thousands of eggs that are roughly handled during shipping and do not develop neurological developmental defects. For rough handling to cause the defect in unrelated eggs they would have to be roughed up during the neural tube development, which does not happen until the eggs are incubating.
Genetics is certainly possible. It could even be that the affected eggs all came from the same duck.
As far as nutrition, when you have a group of animals some get more of the resources than others. If there is only a certain amount of food offered, the top dogs get what they want first, and everyone else gets what is left, and if there is not quite enough the bottom feeders get shorted - and those may have deficiencies that the higher-placed individuals do not have. And, as said above, free range does not mean quality pasture - it could easily mean 1 hour a day on a dirt lot.
Choline is another vitamin deficiency that can lead to neural tube defects.