Not sure how Maschine uses them in practice. But they are side-chain inputs, of some sort. You can send audio signals into Maschine, perhaps to trigger things, utilize some signal processing, or manipulate parameters based on tracking dynamics or pitch... again, not sure. But I bet the manual will have info on the exact functionality.
Setting these values makes SONAR ignore those extra inputs.
Also, I should mention: next time you run a VST scan on Maschine, SONAR will count those inputs again and overwrite your manual settings. You'd need to adjust them again.