Preheat oven to 350 degrees. Line 18 to 20 cups of 2 standard (12-cup) muffin pans with baking cups. Sift cocoa, flour, sugar, baking soda, baking powder, and 3/4 teaspoon salt into the bowl of a mixer. Beat on low speed until just combined.
Raise speed to medium, and add eggs, buttermilk, water, oil, and vanilla. Beat until smooth, about 3 minutes.
Divide batter among baking cups, filling each about two-thirds full. Bake until tops spring back when touched with a finger, 20 to 22 minutes. Let cool completely in pans set on wire racks.
Place a mound of whipped ganache (about 3 tablespoons) on top of each cupcake, and frost each using a small spoon or a small offset spatula to create swoops.
Unfrosted cupcakes can be stored at room temperature for up to 1 day.