Assuming I have multiple nukes ready at different ghost academies, when I launch a nuke, which one will be used? There are times when I want to choose the nuke to use, for example during a base race where I'd like to use the ghost academy that will be killed first.
No, there is no way to choose your nuke. They are launched in sequence. Meaning the nuke you build first gets shoot first.
This means you can choose the order before you build them, but you cannot change it afterwards.
Source: I opened a game, build 2 silos and tried everything to change the order. There just is no UI to change the order. I even tried to select 1 Ghost and 1 Silo while launching, still no effect.