Preheat the oven to 350°F. Line 24 standard muffin cups with paper liners and set aside.
In the bowl of a stand mixer fitted with the whisk attachment, or in a large bowl with an electric mixer, combine 12 ounces Coca-Cola®, ½ cup milk, ½ cup vegetable oil, and 1 tablespoon pure vanilla extract. Mix briefly to combine.
With the mixer on low speed, add 3 large eggs one at a time, beating after each addition until incorporated. Scrape the bowl as needed.
Add ¾ cup sour cream to the wet mixture and mix until fully incorporated. Scrape the bowl again if needed.
In a separate large bowl, whisk together ¾ cup unsweetened cocoa powder, 1 ½ cups sugar, 2 ½ cups all-purpose flour, and 1 ½ teaspoons baking soda until evenly combined.
Gradually add the dry ingredients to the wet ingredients with the mixer on low, mixing until just combined and no large streaks of flour remain. The batter will be thin.
Evenly divide the batter among the prepared muffin liners (about 24), filling each about two-thirds full.
Bake 20–25 minutes, or until a toothpick inserted into the center of a cupcake comes out with only a few moist crumbs. Remove the pan from the oven and place it on a wire rack.
Let the cupcakes cool completely in the pan on the wire rack before removing them from the muffin tins.
For the frosting: in the bowl of a stand mixer fitted with the paddle attachment, or in a large bowl with a hand mixer, beat 2 cups unsalted butter (room temperature) on medium-high speed for about 5 minutes, until pale and fluffy.
With the mixer on low speed, slowly add 1 ½ pounds (24 ounces) sifted powdered sugar, adding a little at a time until incorporated. Once all powdered sugar is added, increase to medium speed and beat for an additional 5 minutes.
Add 2 teaspoons pure vanilla extract and 6–7 tablespoons maraschino cherry juice to the butter-sugar mixture. Blend on low until moistened, then beat on medium-high for about 2 minutes until the frosting is smooth and fluffy.
Pipe or spread the frosting onto the cooled cupcakes.
For the chocolate glaze: in a small saucepan over medium heat, warm ½ cup heavy whipping cream until very hot and steaming but not boiling. Remove from heat.
Place 4 ounces chopped bittersweet chocolate in a heat-safe bowl. Pour the hot cream over the chocolate and let sit for about 5 minutes. Whisk until smooth.
Whisk in 2 tablespoons honey and 2 teaspoons pure vanilla extract. Allow the glaze to cool for about 5–10 minutes, until slightly thickened but still pourable. Do not let it harden.
Spoon the glaze over the frosted cupcakes, allowing it to drip down the sides a little. Work quickly before the glaze sets.
If desired, top each cupcake with a maraschino cherry.
Store the cupcakes in the refrigerator. Remove them to room temperature about 1 hour before serving.