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I recommend against using color foods for young fish, but if it is just a small percentage of the total amount fed, it should not matter. I think it best for the color pigment of young fish to develop in its own time.
I suspect there is a problem with your testing. Unless all of your koi are quite small, or you are doing tremendous amounts of water changes, there should be some nitrate being produced by the filtration system.
If water temperatures are above 70F, water is in good condition and they are fed as much as they actually eat, they will grow. If growth is a problem, I'd suggest focusing on getting the water as good as you can.
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