Chickens begin creating their own heat from the moment of fertilization and yes, it does affect the temperature inside the incubator. However, to what degree is based on too many variables that are all different with every single hatch - so you'd never be able to put a blanket statement on how it affects the incubator's temp.
I don't want to get in trouble for citing all sorts of info that isn't mine - it's in the books I read. I suggest ALL of these.
Sources:
Raising Chickens for Dummies
A.B.C. of Poultry Raising
Regarding Chickens: Essentials for the Flock Owner (DVD but I only watched half of it because my DVD/VCR combo kicked the bucket)
A Guide To Better Hatching it's an "okay" book but not my favorite.
Keep Chickens! Tending Small Flocks in Cities, Suburbs, and Other Small Spaces - hilarious book (I use this one when I need to laugh because all the other more important books stressed me out)