I'm faced with a choice of buying either two mono or a single stereo Triple C.
My question is: if I use the digital I/O to process a signal, can I route a stereo digital signal into one mono unit, compress just one side and then run the output of that unit to the digital input of the other unit to compress the other channel before going back to my DAW?
No, unfortunately it's not possible to run a stereo signal through the Triple-C single channel, under any circumstances.
The Single Channel's digital I/O is routed exactly as its analog I/O, where the Direct Output (the one that sits in the same place as the stereo version's right output) is taken directly from the unprocessed left input. So, your "stereo" signal from the first mono unit would consist of 2 left channels, one of them unprocessed.
Please note: The Triple-C is now a discontinued product.