What's the ideal positioning for analog MUX in microcontroller circuit? (in a design with two boards)
One problem with IDC cables is grounding and noise issues, they need to be accounted for or there could be problems with the design.
IDC cables can have cross talk between conductors, so sending the digital signals over IDC could potentially bleed into the next pin if the signals are switching and create noise (I've had this happen before).
With IDC, grounding can become an issue, the IDC is something like 26 or 28AWG which means at least ~50mΩ per foot (plus a few more 10mΩ's for the connectors on each end). If you send a 10mA signal that is switching digitally (or an IC that swtiches 10mA of current on board 2), then the ground could move ~500uA and that is almost 1bit for a 12bit ADC at 3.3V. So make sure the ground is solid by using more than one conductor (use a lot more than one pin).
Unless cost is a major factor, I'd just put one or more cheap ADC's on the other board like the ADS7952S
The best option would be to put the processor on the same board and make the IDC short as possible