Preheat the oven to 350 degrees F.
Line 1 (12-cup) muffin tin with 12 paper muffin-tin liners and place 4 paper muffin-tin liners inside another muffin tin. Add 2 tablespoons of water to each of the paperless muffin wells.
In the bowl of an electric mixer, combine the flour, sugar, cocoa powder, baking soda, and salt. Add the remaining ingredients, adding the hot water last. Beat with an electric mixer until smooth.
Divide the batter evenly among the paper muffin-tin liners.
In a small bowl, beat the cream cheese with the sugar. Fold in the chocolate chips and coconut.
Drop the cream cheese mixture into the center of the cupcakes.
Bake for 20 to 25 minutes, until the cupcakes rise and a toothpick inserted into the center comes out clean. Remove from the oven and transfer to a wire rack to cool completely.
In a small, heavy saucepan, bring the cream to a bare simmer over low heat.
Place the chocolate pieces in a medium bowl. Add the cream into the chocolate and let sit for 3 minutes. Add the vanilla and whisk until the chocolate melts and the sauce thickens.
Drizzle chocolate sauce over cupcakes when serving.