The cue signal can be heard on the main channel on Twitch, but only during streams using OBS. The S4 MK3 mixer itself is working exactly as it should.
The issue occurred suddenly during a stream and persists even after the latest Traktor update.
I hate to say it, but the most easy solution is just to put a cable from booth out to one of the inputs.
Would be cool if traktor could send master / record out to a different audio interface, or software sink device. But nah.
It's how I streamed via OBS. You can try something like ASIO4all or Audio banana .. but in the end it was not reliable and I just choose the cable method. Sucks but what can you do. ¯\_(ツ)_/¯