My assumption has been that the Consult has been working hard for the last few thousand years to rediscover and understand tekne knowledge that was lost, and applying it in new ways. Thus the appearance of skin spies (improved biotech) and nukes (improved understanding of physics)
Indeed, I speculated on that earlier I think. As for the "why now" question on suddenly "developing" a nuke, I think that there are some plausible reasons why they such a thing wasn't used previously.
First, during the Apocalypse, they had the No-God. Bakker loves his, "when you have a hammer, everything seems like a nail" analogy. Why should they have needed more? We get the benefit of hindsight here that they should have obviously needed more, but at the time, attrition probably seemed like a pretty good strategy. Since the Consult couldn't find/get back the Heron Spear, there was reason to believe it might have been just totally lost. They rolled the dice wheeling out the No-God itself and lost that bet. Nothing that they lost though was irreplaceable though, from what they said even during tDtCB.
Second, I actually think this nuke was far more of a one-off thing than anything else. A fuel cell or whatever, rigged up so it could be detonated. It's the proverbial kitchen sink. So, why now? Well, because Kellhus is a real danger to actually kill the Consult, not just foil their plans. This was not a real danger during the First Apocalypse. The Consult knew that the Ark was unassailable. But now? I don't think they are so sure. It's time to find everything not nailed down and start throwing it in Kellhus path, hoping it somehow screws up his plan.