That story is just a popular nonsense with no scientific basis. There's no reason to think that blonds will "disappear in 200 years" or whatever that hoax 'news story' reported. Not even redheads are showing any signs of dying out, even though red hair is a trait transmitted through a recessive gene that only 4% of the human population have. It sounds more like paranoid nonsense than anything. For that matter, straight hair, lack of pimples and freckles, and baldness don't show any signs of disappearing either, and those are recessive genes, too...I so agree with your part here about national boundaries disappearing in the future. I would imagine that, by the time of Kirk and Spock, to be realistic, the cast should be multiracial to reflect that. Have a cast of Barack Obama, Jessica Alba, and Tiger Woods. The Nordic blondes have only about 100 years or so to go before they're a thing of the past.
Mobility of population and diminished importance of boundaries only leads to more diversity, rather than less.
You don't understand what happens when people get to travel to the other ends of the earth, do you? On a more limited scale, it happens to soldiers from time immemorial until now.
They meet and fall in love (or at least lust) with the natives. Differences will be bred out of humanity, not preserved.