For the filling:
Place all ingredients in a medium microwave-safe bowl and microwave until mixture is warmed, about 30 seconds. Whisk until smooth. Place mixture in refrigerator until just chilled, no longer than 30 minutes.
For the cupcakes:
Place chocolate and cocoa powder in a medium heatproof bowl. Pour hot coffee over mixture. Cover and let stand for 5 minutes. Whisk mixture gently until smooth then transfer to refrigerator to cool completely, about 20 minutes.
Meanwhile, preheat oven to 350°F. Line a standard 12-cup muffin tin with foil or paper liners.
Whisk flour, sugar, salt, and baking soda together in a small bowl.
Whisk oil, eggs, vinegar, and vanilla into cooled chocolate mixture until smooth. Whisk in flour mixture until smooth.
Using a spring-loaded ice cream scoop or a large spoon, divide batter evenly among prepared muffin cups. Place 1 generous teaspoon of ganache on top of each batter-filled cup. Bake until cupcakes are set and firm to the touch, about 17 to 19 minutes. Let cupcakes cool in pan on a wire rack for 10 minutes before removing from pan to cool completely, about 1 hour. Cupcakes can be stored in an airtight container at room temperature for up to 1 day.
For the frosting:
Combine sugar, egg whites, and salt in the bowl of a stand mixer. Set bowl over a saucepan filled with 1-inch of gently simmering water. Whisking gently and constantly, heat mixture until sugar is dissolved and mixture is slightly thickened and foamy and registers 150°F on a candy thermometer or a digital thermometer, about 3 minutes.
Fit stand mixer with whisk attachment and beat egg white mixture on medium speed until slightly cooled and thickened, about 2 minutes. Add butter, 1 piece at a time, until smooth and creamy. Add chocolate and vanilla and mix until combined. Increase speed to medium-high and beat until light, fluffy, and well combined, about 30 seconds, scraping down the sides of the bowl as necessary. Frosting can be made 1 day ahead of time and stored in an airtight container in the refrigerator. Warm frosting in the microwave for 5 to 10 seconds and stir until creamy again before frosting cupcakes.
If desired, spoon frosting in a piping bag fitted with a large star tip. Frost about 3 tablespoons of frosting over each cooled cupcake and serve.