Place an oven rack in the center of the oven and preheat to 375°F. Line a light-colored baking sheet with parchment paper.
Remove the cookie dough from the refrigerator. If needed, let it sit at room temperature just until soft enough to scoop. Working with one cookie dough ball at a time, gently flatten it into a thick disc. Place a frozen pistachio–kataifi ball in the center, then wrap the dough up and around the filling, pinching to seal. Roll gently between your palms to form a smooth, tight cookie dough ball. Be sure the filling is completely enclosed so it doesn’t leak during baking.
Place the dough balls on the prepared baking sheet, spacing them about 3 inches apart. Top with chopped pistachios.
Bake until the edges are set and lightly golden while the centers remain soft, about 10-12 minutes. If desired, press a few extra chocolate chips onto the tops and sprinkle lightly with flaky sea salt. If the cookies spread unevenly, use the side of a fork or a round biscuit/cookie cutter to gently nudge them into a more circular shape as soon as you take them out of the oven.
Let the cookies cool on the baking sheet for 10 minutes, then transfer to a wire rack to cool completely. Repeat with the remaining dough, using a cooled baking sheet lined with fresh parchment.
Store leftover cookies in an airtight container at room temperature for up to 3 days.