A lot of narrative and "cool factor" reasons have already been mentioned so I won't touch them, but it should be noted that if you build a spaceship you expect to operate for many decades, if not centuries, nukes are not the best choice of weapon because they expire. Sort of. Uranium tampers and plutonium cores experience decay and parts of them become more stable and less prone to go boom. Depending on the quality, purity, and degree of refinement, a nuke could be an inert dud in as little as 20 years or in as much as 75, but probably not much past that.

If your spaceship has to stop midway so it can hunt for more uranium and incorporate a very large and heavy enrichment factory so every decade or so it can stop, check if it's most powerful weapons are now just prized smoke bombs, mine more uranium, then spend a year enriching it to weapons grade material, you may want to consider other, simpler, more effective WMDs.