I have doubts about the rough handling being the culprit.. and here's why
Peach told me that the other ducklings (from her eggs) hatched fine alongside these eggs in the same incubator.. one would think that if Peach had mishandled the eggs that the same defect would have also been seen in her eggs.. not to mention that you would have better odds of winning the lottery than to have the exact same defect in three ducklings and no other signs of defects from mishandling..
Also.. when eggs are shipped either they develop and survive or they don't.. when a growing embryo hits damaged tissue it dies since it essentially bleeds to death.. so either the egg will develop to term or it won't with shipped eggs... there isn't a middle ground where the exact same defect will arise from simple mishandling of the box by the USPS.. lol.. having hatched out thousands of shipped eggs I have NEVER had a defective bird hatch with the same issue that Peach had (any defects were either genetic or dietary such as crossbeak)
As for a genetic issue.. dietary deficiency is still the more likely cause.. simply because most genetic issues will crop up as cross beak chicks or those with extra limbs.. for all three ducklings to have the exact same issue points more to a folic acid issue than to a genetic one..
Now you may ask .. if she had 10 ducklings from those eggs hatch and only three had the issue.. WHY? (I don't know how many hatched for the record).. well.. quite simply it's because some ducklings are more susceptible to dietary deficiencies than others.. like a Niacin deficiency.. you can have an entire flock of ducklings on feed that is a bit lacking.. yet only a handful will show symptoms..
The breeder probably is unaware of any issue.. it may be that they are having their feed mixed for them and the last batch was missing a key ingredient.. or even a bad batch from the feed mill of prepackaged feed.. I know we have starter feed from our local feed store that is hit or miss on Niacin.. fine for chicks.. but you can't trust it for ducklings simply because you never know when it may be running a bit short on the Niacin.. so I have to buy feed for any ducklings from a different supplier instead of taking the chance with a bad bag of feed