Preheat the oven to 350ºF. Line a standard 12 cup muffin pan with paper liners.
Make the cupcakes: In a large mixing bowl, whisk together the flour, cocoa powder, baking soda, and salt. In a separate mixing bowl, whisk together the sugar, dairy-free milk, vegan mayonnaise, and vanilla. Add the wet ingredients to the dry and stir to combine.
Divide the batter evenly among the prepared muffin cups. Bake for 20-25 minutes or until the tops of the cupcakes spring back when lightly touched and a toothpick inserted into the center comes out clean. Let cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.
Make the filling: Chop the frozen cherries. Place them in a small pan with the sugar and lemon juice. Stir to combine. Let sit for 10 minutes, then bring to a boil, reduce heat to medium low, and simmer until thickened, 10-15 minutes. Let cool.
Make the frosting: Melt the chocolate chips in the microwave or over a double boiler. Let cool at room temperature about 10 minutes.
Beat the shortening with an electric mixer until smooth. With the mixer on low, gradually add the powdered sugar and vanilla. Add the dairy-free milk, 1 tablespoon at a time, and beat until the frosting reaches a spreadable consistency. Add the melted chocolate and beat for 2 minutes or until the frosting is light and fluffy.
Assemble the cupcakes: Using a spoon, make a hole in the top of each cupcake and scoop out about 2 tablespoons of the cake. Crumble the cake into fine crumbs and reserve. Fill the holes with the cherry filling. Frost the cupcakes with the frosting and top with the crumbled cake crumbs. Garnish with gummy worms.
Store the cupcakes in the refrigerator. For best flavor, allow to sit at room temperature for at least 10 minutes before serving.