Sorry if I offended anyone with the "fake" and "sleazy" editorial comments regarding the thermocouple inputs on the NI DAQ products. But it is not exactly a robust or highly accurate method of handling thermocouple signals. There's an assumption that the terminals are at the same actual temperature as the junction, which is probably reasonable. Also, your thermocouples aren't isolated like a dedicated pre-amp typically is. For example, take a look at the AD part for thermocouple signal conditioning:
http://www.analog.com/en/prod/0,2877,7B27,00.html
They also use an external thermistor as part of the signal processing. but the output is isolated from the input, and is already low pass filtered to allow slow data collection speeds without aliasing.
But the cold junction compensation scheme is really not an issue, because if anybody is interested in highly accurate or precise temperature measurements, they shouldn't be using thermocouples in the first place.
Sheldon
Technical geek, engineer, research scientist, biodegradable...