Because whatever way you look at physics, the release of nuclear energy is a very real phenomenon which occurs throughout the Universe (hydrogen-> helium fusion within stars, being the most obvious answer).
You can approach physics from an infinitely advanced perspective, but it does not change the broad effect of what is physically realisable. For example... We know (now) that Newtonian physics is merely an approximation which is valid within a fairly limited range of mass, energy and length-scales. BUT, even when you understand quantum mechanics, relativity and (say) quantum mavity, it does not alter the fact that when you apply a force to an object, it moves relative to an inertial frame with a quantifiable acceleration (a ~ F/m).
You can supersede a technology, and understand more thoroughly where it comes from, and why it works the way it does, but that does not change the fact that it exists and is observable.