Hey.
Smoothieboard's pins are read by an ADC ( Analog to Digital Converter ), which is one of the peripherals of the microcontroller.
The thermistor inputs have two connections : one to AGND ( a Ground specially for analog inputs ), and one to the actual ADC pin on the LPC1769.

Why do you need to know ?

Cheers

Subbed. Curious about application as well. 

I try to combine some wires / voltage rails to reduce the amount of individual wires running to the hotend. While I am able to combine the 24V rail and just seperate GNDs for heater, fan, etc I was wondering what can be about the thermistor. I already read the schematic and just wanted to make sure. 

You can have several thermistors sharing the same AGND if you really need to. But you can't have AGND and GND mixed up, that'll mess up your temperature reading.

ok. Thx for the input +Arthur Wolf

Yes.  From someone who has been doing the electrical layout of these things for the last month, KEEP YOUR AGND SEPARATE!