You have an extremely nationalist leadership with a guerrilla arm which exists throughout Vietnam. If you cut the head off, you don't kill the body. You've basically just scattered everything around and are dealing with guerrillas that can no longer be negotiated with. That's just the tactical problem. You also have the problem of public relations. Using atomic weapons would make the United States look unbelievably bad, and there is no telling how easily the Communist bloc would decide to go all in for the defense of North Vietnam themselves (depending on the time period). And nuclear arms usage is very hard to avoid escalating into WW3. Barring WW3, you at least remove the trepidation of using atomic weapons at least somewhat, which could lead to them being more easily used (say, the Soviets using them for Afghanistan were that to still happen) which in turn leads to atomic weapons being less feared and thus more used and thus less feared and thus more easily used and so on and so on, and that can have dire consequences.