WD40 was actually developed as a water displacement formula to prevent corrosion in rockets and nuclear missiles in 1953. Though many use it as a "solvent" to loosen rusted nuts/bolts, it is actually a lubricant.
From Wikipedia: "The long-term active ingredient is a non-volatile, viscous oil which remains on the surface, providing lubrication and protection from moisture." so indeed, you could use it on the fan in the incubator. It would also serve to prevent moisture from damaging the motor, just like virtually any machine oil. Unless you "coat" the eggs in oil, I doubt a little spot of oil on the shell will hurt the developing embryo. Of course I could be wrong and you might end up hatching out a miniature Godzilla or something similar, or some deformed chicken...