You can probably find the specifics on google especially if you look up an individual supplement, but the long story short is through years of observing and testing like anything else. With decades and decades of blood tests, we can find what is a recommendation based on healthy and unhealthy tests. Then you start with a range and fine tuning that range to get something more exact.
Keep in mind that even with recommended values, everyones body is still unique and individual and what you actually may need will vary. But generally the vast majority of humans can have a healthy life following recommendations.
It depends. For the “essential fatty acids,” the USDA could not determine a minimum required amount, so they just recommend that people eat the median amount the population is already consuming. Basically, “What you’re doing appears to be working, so just continue doing it.”