EMP's have been shown to wreak havoc on nanites, so a high-alititude nuclear explosion could wreak havoc on nanite systems (heh) below. On the ground, it would probably just blow them to smithereens unless they were supplied with enough energy to throw up a shield against the blast. This shouldn't be too difficult since it seems we've mastered fusion and battery technology.
Interestingly, there are references to weapons of mass destruction in the lore. I'm wondering why we don't see them now. My theory is that the VS had something to do with it. In the early years of this war, the NC and TR were reenacting humanity's previous war, flinging nukes at each other until one of them couldn't fling back. Fusion powered nanite shields and anti-missile weaponry prevented the two factions from being wiped out, but not Auraxis. The planet was sustaining heavy damage to its ecosystem, not to mention the Vanu ruins deliberately nuked to prevent the closest faction from obtaining its technology. At the time, the VS and NC were allied against the TR, a common enemy. The VS were providing the NC with technology. The NC find a way to use whatever technology the VS were supplying them with, perhaps antimatter reactors or zero-point energy generators to power their anti-nuke shields, into a superweapon several orders of magnitude more destructive than a nuke that would wipe the TR from the face of Auraxis. More accurately, wipe off the face of Auraxis with the TR still on it. The VS, already angered by the NC's abuse of Auraxis, are kept in the dark about this and are infuriated at this grotesque twisting of their sacred Vanu technology. They break up with the NC by sabotaging the rebirthing matrix of their most secure base, Hossin, which leads to these entries.
www.reddit.com/r/Planetside/comments/29770l/deputy_directors_journal_june_25th_2859/
https://forums.station.sony.com/ps2/index.php?threads/update-notes-06-26.191225/
They destroy both the TR and NC's space based WMD's and launch an anti-satellite web of their own. The VS like to think of themselves as morally justified for doing this, but are they really? 10+ years later, we're still fighting with no end in sight. Perhaps it would have been better to end the war right there in a decisive cataclysm, cutting short all the suffering of the past decade and foreseeable future.
If space combat is ever added, this could be a neat template for lore based gameplay attacking/defending nuclear platforms.