Your confusion may stem from the fact that you don’t realize you’re conflating two different kinds of data sources.
When the USDA analyzes a food, they test it to see what exactly is in the natural product. This is expensive and time consuming, so we do it by having a government organization do the work for various raw ingredients and publish the result for public use by everyone. You don’t have to analyze a pancake, because the USDA has already analyzed butter, flour, egg, milk, sugar, salt, and baking powder. You can measure the ingredients, and infer what’s lost due to heat degradation, and voila.
But when a food manufacturer produces a Nutrition Facts label, they do not analyze their product for everything. If they did, the product would be much more expensive… and the laws do not require them to analyze the product. The law requires them to list the amounts of certain important macros and vitamins, and the rest are completely optional - unless they have manually added them as a supplement. So if your whey adds niacin to the mix, it must be listed as an ingredient on the label, and it must show the DV. But if no niacin is added, then they don’t have to have a DV at all. The “-” doesn’t necessarily mean zero.
The only micros that are always required are sodium, calcium, iron, Vitamin A, and Vitamin C. The new guidance will drop the requirement for Vitamin A and Vitamin C (because deficiencies are rare), and will instead require the listing of Potassium, and Vitamin D. All the rest of the micronutrients are optional… unless they are added as ingredients. (Or unless the product packaging touts it as being a “food high in so-and-so…” if they write that on the box, they have to accurately list the amount of the item.)
So when you look at a food manufacturer label, it will skip most of the optional micros. And when you look up a food in the USDA database, it will have all the available information from studies that have been done.
And when you look at SELF’s NutritionData, you will find entries from BOTH sources, and it’s not obvious which one you’re looking at!
If you look up a food ingredient on SELF’s site, you will usually get the USDA analysis info. If you look up a food product made of multiple ingredients, you’ll usually get the manufacturer’s label information. In my experience, everything that shows up as “custom” has been taken from a food label, and will have incomplete information:
While things taken from the USDA database (or perhaps other authoritative sources) will show like this:
You provided the link for whey as: http://nutritiondata.self.com/facts/custom/1360377/2. That’s got “custom” right in the URL; it probably came from a food manufacturer’s label.
You might also look at this: http://nutritiondata.self.com/facts/dairy-and-egg-products/101/2. That’s the entry for the ingredient Whey, dried, acid. This has a rather complete nutrition profile. At the bottom, it explicitly says that the source is the USDA:
Notice that the “-” means missing or incomplete, it does not mean “0.0”…
Of course, 100 g of the custom isolate has 88 g of protein… while 100 g of the ingredient whey has 12 g of protein. For the custom isolate, the carbs from the whey have been removed, concentrating the remaining ingredients… assuming that the Niacin is not lost in the carb-removal process, then you’d need 88/12 = 7.33 times as much pure whey to get to 88 grams of protein - that’s 733 g of whey - so you’ll have 7.33 times as much Niacin. The Whey has 1.2 mg of Niacin per 100 g, implying the custom isolate may have around 1.2 * 7.33 = 8.8 mg of Niacin per 100 grams of product.
Fortunately, there are precious few items on which you need have any concern about over-consumption. You do want to know the true macro content (and all labels list the macros accurately), and you want to avoid excesses of things like sodium (again, always listed.) There are very, very few areas where hypervitaminosis is a real concern from consumption of normal foods… if a deficiency or an excess happens with any frequency in the population based on normal food consumption, then that item is required to be listed on labels. That’s why Iron is required to be listed (many people are deficient) and Sodium is required to be listed (many people get too much.) For the other items, hypervitaminosis is only observed when people take the substance as a supplement, and usually only when they take Super-Mondo-Mega-Product!
Most of the micros that have notable risk when you take too much - like Manganese - are not common as sole supplements, and are in multivitamins in very small amounts. That’s no accident.
For things like Niacin - and, indeed, all the water-soluble B vitamins - you don’t need to worry about reasonable excesses at all… even several times the DV. In fact, there’s good evidence that an abundance of them (well above the DV) is beneficial.
The DIY soylent calculator has “Max” values built in on those nutrients where we may have concerns about higher dosages, especially on items where people commonly use high-potency supplements, or on items where normal foods may get you high levels naturally.
If you’re looking for more information about specific vitamins, I highly recommend: