Why are the junctions where ADC pins connect to PCB board ignored in thermocouple cold jucntion conmpensation calcutaions?
It is the junction between the exotic thermocouple alloy wires and the "real-world" that is the source of the cold-junction error factor. Once the signal has proceeded through that junction, it is just like any other millivolt signal. 

Here in modern times we have special chips that measure the cold-junction temperature and apply the correction factor. You kids don't know how nice you have things these days!  :-)