I've found that hatcheries do not seem to generate the loot chickens should drop (lapis, iron, flint, etc) while they do generate eggs and manure.
I see this issue in sky factory 3 after FTB updated the mod. I am not sure if this is unique to skyfactory.
I looked at the configs and everything looks fine. others have this issue, as everyone on the server has reports this.
If you need any more info, please let me know. thanks!