For the ganache: Put the chips in a medium bowl. Heat the heavy cream in a small saucepan just until it bubbles around the sides. Immediately pour the hot cream over the chocolate, give the bowl a good shake and let stand 10 minutes, shaking the bowl occasionally. Then whisk until the mixture is homogenous, 20 to 30 seconds. Chill about 40 minutes, stirring occasionally and scraping down the sides, until the mixture is almost spreadable. Give it another brief whisk, and let stand at room temperature until it's at frosting consistency.
For the cupcakes: Preheat the oven to 325 degrees F. Line standard muffin pans with 20 cupcake liners. In a small bowl, stir the chocolate chips into the hot espresso until melted; cool in the refrigerator to room temperature.
Sift the flour, cocoa powder, baking powder and salt into a bowl. In the bowl of an electric stand mixer with a paddle attachment, beat the eggs, granulated sugar, applesauce, oil and vanilla at medium-high speed for about 2 minutes. Beat in the cooled chocolate mixture until the mixture is homogenous. With the mixer on medium-low speed, add the flour mixture and beat just until incorporated, scraping the sides as necessary. It's ok if the batter is slightly lumpy. Using a 1/4-cup ice cream scoop, fill each cupcake liner with batter.
Bake until a cake tester inserted in the center comes out with a few moist crumbs attached, 18 to 20 minutes. Transfer the pans to cooling racks and cool for about 10 minutes, and then transfer the cupcakes to the racks to cool completely before filling and frosting.
While the cupcakes cool, make the filling: In the bowl of an electric mixer fitted with a whisk attachment, whip the cream and confectioners' sugar to firm peaks. On low speed, whisk in the espresso. Use immediately, or hold in the refrigerator until ready to assemble.
To assemble: Use an apple corer or melon baller to remove the center from each cupcake, about three-quarters of the way into the cupcake. Use a pastry bag to pipe some of the espresso cream filling into the centers. Pipe a large rosette of dark chocolate ganache on top of each cupcake.
Tip: Applesauce replaces some of the oil and sugar in these cupcakes to bring moisture and sweetness to the table.