That shouldn't make a difference. If anything, it should help as it would better match your screen to the ambient light, allowing you to make better choices.
I've heard a lot of people in graphics who use f.lux or redshift only to turn it off when they do graphics work, but I find more accurate results if it is left on. This calls for another experiment!
It will make a difference. Your eyes can see a much wider color space than your monitor can display. By shifting colors, f.lux leaves some of the monitors color space unused, compressing the remaining colors so that some are closer together (or the same even).
Not shifting it still leaves some of the monitor's color space unused. I want to see data.