Put 1/4 cup pretzels in a resealable plastic bag and crush into coarse crumbs with a rolling pin.
Beat the butter and sugar in a large bowl with a mixer on medium-high speed until light and fluffy, 3 to 5 minutes. Whisk the egg yolks, honey, vanilla and fine salt in a medium bowl, then add to the butter mixture and beat until incorporated, scraping down the bowl as needed. Reduce the mixer speed to low; add the flour and pretzel crumbs and beat until just combined.
Put the remaining 1 1/4 cups pretzels in the resealable bag and roughly crush with the rolling pin; spread on a rimmed baking sheet. Drop tablespoonfuls of dough on top and roll into balls, pressing so the pretzels adhere. Refrigerate until firm, about 30 minutes.
Position racks in the upper and lower thirds of the oven and preheat to 325 degrees F. Line 2 baking sheets with parchment paper. Arrange the cookies about 1 1/2 inches apart on the prepared baking sheets; make a deep indentation in each with your thumb. Bake, switching the position of the pans halfway through, until lightly golden, 15 to 18 minutes. Re-indent with the back of a teaspoon, if necessary. Let cool 3 minutes on the baking sheets, then transfer to racks to cool completely. Fill each indentation with dulce de leche and sprinkle with sea salt.