Vaccinations against Merek's at least can still mean they are carriers for it and therefore the chicks could get it. Cocciodosis is a parasite and can exist in the dirt and soil. I don't have a complete knowledge of either vaccine, especially cocciodisis, but I know you can only buy a 1000...
Take a deep breath, sit back, and enjoy the ride! Mama knows best :) Congrats are your babies!
Probably not all will hatch, but mamas usually have a much higher hatch rate than incubators.