You should be able to do that with right mapping - meaning you would probably need to remap S2 to control decks C and D. But keep in mind that Traktor will connect to only one audio interface at a time.
I just tried it with my S5 plugged into one port on my Z2. Worked surprisingly well. All effects and EQ’s worked on both pieces of eqpt. The Z2 channel A fader and Channel C knob controlled the output, and all faders were off on the S5. Like Stewe said, mapping C and D to the S2 might be all you need. Seems like all other controls will work. Post up when you’re done. Would be cool to see.