Nope, not usually.
The break-in is for the upper (usually leather on boots and mostly around the ankle-flex point) and mid-sole (in between the walking-on sole and insole). This also applies to the area around where you lace up (lots of material over-lap in/around the tongue and lace structure).
Actually, a nylon shank helps make for a warmer boot than a "steel" shanked boot and can be better - depending on the use/weight of the wearer.