There are hints that the rise in magic has altered nuclear reactions in some way, possibly by the existence of new particles that require a certain magic level. Nukes (as shown by Cermak, or by Winternight's nukes) still work, mostly. I am intrigued by fusion tech only being developed after the Awakening, but that could be unrelated parallel tech development. Dunkelzahn did set aside some nuyen in his will towards researching the link between nuclear energy and magic, though.
The Lone Eagle nuke flat-out didn't go off, suggesting something else happening there. The Aztlan SB hinted that someone may have been providing info to Howling Coyote and others to further their own goals... I wonder if they may have nixed the missile somehow because the possibility of escalation into full-scale nuclear war didn't fit into their plans.