I just tried a test with an 8-channel file. Using my headphones plugged into my computer, I observe exactly the behavior you request: CH1 is in the left and CH2 is in the right. CH3-CH8 are ignored.
I would suggest that you turn on the “Audio Peak Meter” in Shotcut and observe whether the left and right meters are changing independently. The are for me.
Also, maybe double-check that your speaker/headphone setup provides stereo separation from other applications. For example, play some files from here and see if you hear the L/R separation:
If none of that helps you, the next step would be for you to post a screenshot of the “Audio” tab from the “Properties” panel for your clip in Shotcut so that I can see exactly what kind of audio you have to reproduce your problem.