I have never had a chameleon hatch with an obvious deformity.
I had one rudis (WC) give birth shortly after her arrival to a ridiculous number of babies...and one of the babies was born kind of folded over mid-spine. It straightened out in a couple of days.
The very first chameleon I ever hatched had a slight bend in her spine that I assumed was the result of the egg being incubated at the top end of the "acceptable" temperature. It was as if when she unfolded she only unfolded 98% of the way. She lived a long time and never had any issues. She was a Chamaeleo chamaeleon.
The only birth defect I ever had in a lizard was a cleft palate in a water dragon.