Gameplay-wise the Horde losing Undercity is a bigger deal, as now they have to rely on going to Silvermoon at the very tip for any business in Northern EK. This is of course assuming that the destruction of both cities will translate into them being unusable in BfA.
The redundant location of Darnassus and Exodar annoyed me for the longest time playing Alliance, I'm glad that one of them being is removed, although it is at the cost of the poor Night Elves.