I actually have a different view on this.
Perhaps both nukes were launched, nuking everything that's been built in the west since the Great War.
Why?
This is Obsidian's way of passing the torch to Bethesda.
Clear out their stuff so Bethesda's free to create what they like, with Vegas being the only remaining trace of the original Fallouts.
Hell, even ED-E can be interpreted as symbolic. Doubt any of this
truly holds meaning (it's very out there), but I still think it's a fun little theory that sort of makes sense:
What is ED-E? The only reference to Bethesda's Fallout 3; eyebots are a Bethesda creation. The Courier? He's Obsidian. He's Interplay that made the mistake of letting things slide. ED-E destroyed the Divide because he was a detonator, and he was allowed to do so due to the Courier's neglect, much like Interplay made mistakes, lost everything and then Bethesda took over, starting something new. Now? Now the Courier walks the road, seeing the consequences of his actions, and as Ulysses says "looks like you can't get rid of your shadow," as ED-E follows him the whole way whether he wants to or not, because Fallout now belongs to Bethesda. And at the end? At the end, perhaps it's time to let go. Don't kill of ED-E, he's got a story of his own to complete, much like Bethesda has lots of plans for Fallout. Nuke the world, give it a chance to start something new, then walk off into the sunset.
We'll see though. They obviously have to pick one, and nuking none or nuking both seems most likely.