In theory, if they had nuclear weapons, and they went unchecked for an extended period of time, they would simply degrade into their silos... becoming toxic in near proximity, but otherwise harmless to the surrounding areas. The problem arises when nuclear weapons detonate, because that spreads the fallout all over, and destroys most biological matter in the blast radius nigh instantly, and disables any device susceptible to E.M.P...
It's not unfathomable that they had them, but I always imagined the pre-'99 planet to be more a peaceful society... That's just how it seemed to me anyway. Maybe that's counter-intuitive based on the shear amount of weapons in 2300AD... Honestly I think it would be more interesting to think about that last 300 years after '99. The 1000~1999 period never seemed like much really happened. I mean science advanced, but everything seemed pretty cozy.
I'd imagine whatever happened in the interim of antiquity and present probably continued to happen for a while... Maybe I'm just too tired right now, but I can't really think of much other than the fall of Guardia and deciding to make cities come in jar format.