Step 1: In a medium bowl, whisk together the all-purpose flour, Dutch process cocoa powder, salt, and baking powder. Set aside.
Step 2: In a large bowl, using an electric mixer, cream together the softened unsalted butter, light brown sugar, and granulated white sugar until light and fluffy (about 2-3 minutes).
Step 3: Beat in the egg yolks one at a time, mixing well after each addition. Stir in the vanilla bean paste or extract until combined.
Step 4: Gradually add the dry ingredients to the wet ingredients, mixing on low speed until just combined and a soft dough forms. Do not overmix. Cover the dough and chill in the refrigerator for at least 30 minutes.
Step 5: Preheat your oven to 350°F (175°C). Line baking sheets with parchment paper. Roll the chilled dough into 1-inch balls and place them about 2 inches apart on the prepared baking sheets.
Step 6: Use your thumb or the back of a small measuring spoon to create an indentation in the center of each cookie. Bake for 10-12 minutes, or until the edges are set. The centers may still look a little soft. Remove from oven and let cool on the baking sheets for 5 minutes before transferring to a wire rack to cool completely.
Step 7: While cookies cool, prepare the ganache. Place the semi-sweet chocolate chips in a heatproof bowl. In a small saucepan, heat the heavy whipping cream over medium heat until it just begins to simmer. Pour the hot cream over the chocolate chips. Let sit for 5 minutes, then whisk until smooth and glossy.
Step 8: Once the cookies are completely cool, spoon or pipe the chocolate ganache into the thumbprint indentations. If desired, sprinkle with nonpareils immediately after filling. Allow the ganache to set before serving. This can be done at room temperature or in the refrigerator for quicker setting.