Nuclear explosions in vacuum don't cause shockwave, but cause extreme and destructive radiation wave (nearly 100% energy go to radiation [Starfish test in 1962]) - and it can work as AoE effect. Because of point defense effectiveness, slow movement speed and overkill issue, missiles are completely useless ATM. Adding AoE damage at significant radius and removing overkill issue (missiles explode at destination place, instead of vanishing after target dies) will effectively turn them into high-risk-high-reward weapon, additionally giving interesting way of interacting doom stacks.
I'm not advocating (yet) any of the other stuff in that SFU, but the Honor Harrington books had their ships operate in fleets where the individual ships were separated by many thousands of miles (even the mile-long ships were invisible to the naked eye at that distance). That's actually not even close to the immense distances between ships in formation in Stellaris, if the visual representation is
anything to go by (and considering that it's counted as actual range in the combat calculations, I'd say it's intended as legitimately that far apart), but it starts to give you an idea.
The warheads of nuclear missiles in Stellaris aren't likely to be that much more effective than similarly sized missiles IRL - I'm not expecting a S-size missile mount to fire a missile much bigger than about 15-25 feet long (no longer than a PATRIOT anti-ballistic missile) and the L-size being no bigger than the Thor that carried Starfish Prime. Even switching over to an exotic explosive and using an XL-size missile isn't going to catch more than 2-3 ships at once, certainly not enough damage on the secondary targets to mean much. And programming the game to have missiles target arbitrary in-between points among the enemy ships to somehow maximize the splash should be real fun.
Doomstacks aren't going to be any more affected by a splash damage missile than any other fleet in formation, as there is currently no difference between the formations of any size fleet. And there's nothing stopping the doomstack from firing the same types of missiles into the opposition fleets, either. And would we even think about the possibility of friendly fire on the splash damage, especially during the furballs?
I think there are enough issues with the actual game programming to keep any idea along this line from going forward, but I don't see it being helpful regardless of any technical feasibility.