What dirves pins.h is the stuff in configuration.h. Depending on what motherboard you have set it'll do all sorts of odd things.
With no Ramps on the Mega, there is no pull up on the ADC input that connects to the thermistor. The only thing you will read is leakage currernt. That reading could be just about anything at all. The Mega reads the thermistor by using a bridge circuit to convert the resistance to a voltage. That's why shorting (or opening) the thermistor pins is a usefull diagnostic. You get max or min voltage on the ADC input. If you don't see a swing from min to max, either you are on the wrong input, your pull up resistor is fried, or the adc input is blown.
With no Ramps on the Mega, there is no pull up on the ADC input that connects to the thermistor. The only thing you will read is leakage currernt. That reading could be just about anything at all. The Mega reads the thermistor by using a bridge circuit to convert the resistance to a voltage. That's why shorting (or opening) the thermistor pins is a usefull diagnostic. You get max or min voltage on the ADC input. If you don't see a swing from min to max, either you are on the wrong input, your pull up resistor is fried, or the adc input is blown.