It won't defeat him in one hit, he'll keep on coming back depending on how many hearts you have.
I find it very fast to finish him off though, and if I wanted to, could probably defeat him in about less than a minute.
The Megaton Hammer is a great weapon and is very efficient against Dark Link, but I find the Biggoron's Sword is more useful against him. Have you even used the Biggoron Sword's thrust move? It is very fast and Dark Link has no way to guard against it. Of course, you might miss a couple of times...