Make the Cookie Dough : In a mixing bowl, cream the softened butter, brown sugar, and granulated sugar together until light and fluffy. Add the egg yolks and vanilla bean paste (or extract) to the bowl, mixing until fully incorporated. Sift the all-purpose flour, Dutch-process cocoa powder, baking powder, and salt into a separate bowl. Gradually add the dry ingredients to the wet mixture, mixing just until a dough forms. Avoid overmixing to keep the cookies tender.

Shape and Chill : Scoop tablespoon-sized portions of dough and roll them into balls. Place them on a parchment-lined baking sheet, spacing them 2 inches apart. Use your thumb or the back of a teaspoon to gently press an indentation into the center of each dough ball. Chill the cookies in the refrigerator for 30 minutes. This step helps maintain their shape during baking.

Bake : Preheat your oven to 350°F (175°C). Bake the chilled cookies for 10-12 minutes or until the edges are set but the centers remain slightly soft. Remove the cookies from the oven and gently press the thumbprints again to ensure a deep well for the filling. Let the cookies cool completely.

Prepare the Ganache : Heat the heavy whipping cream in a small saucepan over medium heat until it just begins to simmer (do not boil). Pour the hot cream over the chocolate chips in a heatproof bowl. Let it sit for 2-3 minutes, then stir until smooth and glossy.

Assemble the Cookies : Once the cookies have cooled, spoon the ganache into the thumbprint wells of each cookie. Decorate with nonpareils or sprinkles while the ganache is still soft. Let the cookies sit at room temperature until the ganache sets, or place them in the refrigerator for faster setting.