I've worried about this too, but isn't this something that can be easily tested? I mean, if nutritionists have really identified the vitamins, etc. we need, divided the thingspace appropriately (are all things called "protein" functionally the same?), and developed reliable ways of measuring nutritional information that goes on the food label, this should show up pretty quickly. (I'm becoming less confident of assumptions like these, in part because of errors like what Phil Goetz found here.)

When standard produce is packaged, how do they get the data for the label? Do they have to regularly test that source's produce, or is there just a standard lookup table that e.g. all baby carrots can give as their data? (If the latter, that screams "information cascade!")