Preheat the oven to 350°F (175°C). Line a standard 12-cup muffin tin with paper liners.
In a large bowl, whisk or beat together 2 eggs, 3/4 cup buttermilk, 1/4 cup plain Greek yogurt, 1/2 cup canola oil, and 1 tablespoon vanilla extract until smooth.
In a separate bowl, whisk together 1 1/2 cups all-purpose flour, 1 1/2 cups granulated sugar, 1 cup unsweetened cocoa powder, 1 1/2 teaspoons baking soda, 1 1/2 teaspoons baking powder, and 1 teaspoon kosher salt.
Add the dry ingredients to the wet ingredients and mix on low speed or fold with a spatula until no visible flour remains and the batter is smooth. Do not overmix.
Stir in 1/3 cup hot black coffee until combined. The batter should be pourable but not very thin. Fold in 1/2 cup mini semi-sweet chocolate chips, if using.
Divide the batter evenly among the prepared liners, filling each about two-thirds full.
Bake at 350°F for 15–18 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs. Remove the pan from the oven.
Let the cupcakes cool in the pan for 5–10 minutes, then transfer them to a wire rack and cool completely before frosting.
For the frosting: In a large bowl, beat 3 sticks (1 1/2 cups) room-temperature salted butter until creamy.
Add 3 cups powdered sugar and beat on low until incorporated, then increase speed and beat until the mixture is light and fluffy, about 2 minutes.
Add 3/4 cup unsweetened cocoa powder and 2 teaspoons vanilla extract. Beat, scraping down the sides of the bowl as needed, until the frosting is uniform in color with no streaks, about 2 minutes.
Add 3 tablespoons heavy whipping cream and whip the frosting for 2–4 minutes until light and fluffy. If the frosting is too thick, add the remaining 1 tablespoon heavy cream (for a total of 3–4 tablespoons) and beat until you reach the desired consistency.
Frost the cooled cupcakes as desired. Store frosted cupcakes covered in the refrigerator for 3–4 days and bring to room temperature before serving.