1. Whisk together flour, baking soda, and salt in a small bowl.
2. Beat together butter and sugar in a large bowl on high speed until light and fluffy, about 2 minutes. Add egg yolks, one at a time, beating well after each addition. Add extract and honey; beat until combined well.
3. Reduce speed to low and slowly add flour mixture, beating until just combined. Fold in chocolate. Chill dough until firm, about 2-1/2 hours.
4. Preheat oven to 350 degree F and arrange rack in center. Line 2 cookie sheets with parchment paper.
5. Roll dough into 1-inch balls and place on prepared sheets about 1 inch apart. Using the end of a wooden spoon, make a dent in center of each cookie. Freeze 15 minutes.
6. Bake 1 sheet of cookies 10 minutes. Remove from oven and redent centers. Fill with generous 1/4 teaspoon dulce de leche and bake until set, about 3 minutes. Repeat with remaining sheet.
7. Transfer cookies on sheets to racks and cool 5 minutes. Using a metal spatula, transfer cookies to racks to cool completely. (Can be stored at room temperature in an airtight container, in single layers separated by waxed paper, up to 1 week.) Makes about 40 cookies.