The staggering amount of released energy from a nuke is not insignificant.
The blast wave associated with them, as far as space goes, is.
Space isn't entirely empty, there's junk floating around out there, but compared to an atmospheric environment, it is.
The point, the blast wave (the principal destructive force from a fission/fusion warhead) is almost utterly irrelevant in a space environment. Gravity is the force it acts against(as it holds the things it passes to the planet) where as the ships you shoot at are only under the forces they are imparting to move.
That said, it is not illogical or ludicrous to set them as an aoe weapon, the sheer amount of released energy in the vicinity males this plausible enough, and lasers themselves are basically just funky colored heat lamps...
Aso far as matter/anti-matter explosions go, who knows. If that interaction is as theorized, those missiles could be ripping apart the fabric of space time.
And let's not forget, that missile that turns to plasma is ejecting said plasma in all directions, or directionally if so designed, which lends to an aoe type result as well.
Wouldn't mind them if they were aoe myself, I'd rather the mere gun come along and make pd less effective against them. That is where I would start tweaking things, and if they can add retargeting into the game, that should also be put in as a tech path (dumbfire missiles vs self guided munitions) for missile empires to pursue.
I'm fine with getting hit with space bullets or heat beams before missiles hit, because flight time need be considered.
But until small amounts of pd doesn't absolutely negate large missile fleets, the other gripes need to take a seat on the back burner.
And yeah persistence should be there too, because missiles don't just vanish...