Since 1945, the general public has been keenly aware of the effect of nuclear weapons within the atmosphere of our planet, but once you take away the atmosphere, the true awesome power of the bomb is robbed in the vacuum. The issue is that 50% of a nuclear weapon's power is from the concussive force (the blast wave), which would not exist in the vacuum of space. 35% is heat, and rest (15%) is the series of nuclear radiation. Atmosphere is the conductor of the destructive power of a nuke, and once you take away that, you are left with a WMD that is only effective (to some degree) within one kilometer of the target! That is damn close in space combat, like living in the underwear of the person you're trying to kill. Not mention, that a nuclear device has to survive through the enemy warship's AAA defenses and any “space fighters” forming a screen.
Internal Nuclear Explosion?
Endoatmospheric nuclear explosions are the stuff of doomsday scenarios and are awesome examples of mankind's technological and scientific progress. However, in the vacuum of space, nuclear weapons lose their fangs. This casts doubt on the utility of nuclear weapons in space combat, but what about an nuke explosion inside the hull of an starship? We've seen this used in the destruction of the Cloud Nine pleasure spaceship in BSG and the teleporting an nuclear warhead inside of a Wrath ship on Atlantis. If I had been in command of the D when the Borg cube came calling, I would have tried to beam over a nuke with the words "assimilate this, fuckers!" That begs the question: would internal nuclear explosion would be more effective than exterior? Certainly.
Future Weapons that could Replace Nuclear Weapons
Relativistic Kinetic Kill Vehicle Weapons (RKKV or R-Bombs)
Matter/Antimatter Annihilation Explosives
What happens when you combine one gram of hydrogen and one gram of antihydrogen? About 43 kilotons of explosive power and a possible replacement for nuclear weapons as seen throughout the Trek universe and been part of scientific research since 1950. While this may seem to a winner to most, but there drawbacks to the use of M/AM collision weaponry. First is that antimatter is extremely expensive, about $25 billion per gram, and it is difficult to contain and manufacture using modern, known means. Then there is the real kicker...there will not be 100% efficiency of the antimatter used for the explosive yield. This means if your photon torpedo, housing 1.5kgs of antimatter should yield 64.3 megatons of explosive yield, but it will not due to some reactions between being harmless and 100% of the antimatter being utilized, causing your torpedoes to be variable in yield. All of this adds up to antimatter weapons being a poor substitute for nukes.
Kinetic Orbital Projectile ("Rods from God")
Beside weapons, another use for nuclear energy is fairly common: power generation. It is not just here on Earth, but also used on space probes when solar panels, fuel cell, or regular batteries are impractical. While several satellites have flown with regular nuclear reactors, the radioisotope thermoelectric generator (RTG) that uses the heat for radioactive decay to generate electricity (about 62 watts) for about 87 years. RTGs have been fitted onto some of the most iconic space probes and Martian rovers throughout space exploration history. Beside the Voyager space probes and the Mars rovers, there were several experimental stations on the Moon that were planted by Apollo missions. Some of the most distant man-made objects, the Pioneer and Voyager space probes are powered by several RTGs and will be for decades to come, around 2025.
Nuclear Rocket Propulsion
World War III from the Mad Max Universe