a friend of mine once told me that when he was doing his practical (university course work) in one of the big biscuit factory in Malaysia, for the factory to apply and obtain the certificate of halal, the factory had to allocate a place for the eggs (ie egg shells) to be washed and cleaned (clean as in urdu "pak" / or in malay "suci") of any najasat. Then the authorities related with the giving the halal certification will send 2 persons, one from the health department and the other from the religious department to inspect the process of making biscuit. In Malaysia, there are muslim restaurants where one can see the najis (chicken's poo / droppings) sticking on the shell and the restaurant chef touch the shells with his hands and then the hands touches other food / utensils etc. In food health term this is called cross contamination. In Islam this is "na pak" / "tidak suci" / unhygenic according to the shariat... Any thoughts on that ?
By the way, I was taught that in the Hanafi mazhab, the excrement of halal birds is not najis. I don't know what is the case for Shafiis. Obviously, you still want to prevent it from getting into food.