Position racks in the upper and lower thirds of the oven; preheat to 350 degrees F. Spread the pecans on a rimmed baking sheet and bake until lightly toasted, 8 to 10 minutes. Let cool completely. Set 24 whole pecans aside for topping and finely chop the rest; transfer to a bowl. Pour 2 tablespoons whiskey over the chopped nuts, stir to coat and let sit until almost all the whiskey is absorbed, at least 10 minutes.
Whisk the rye flour, all-purpose flour, baking powder, baking soda and salt in a medium bowl. Beat the butter and brown sugar in a large bowl with a mixer on medium-high speed until light and fluffy, 2 to 3 minutes. Beat in the pecan-whiskey mixture and the vanilla until just combined. Reduce the mixer speed to low; beat in the flour mixture until combined.
Line 2 baking sheets with parchment paper. Roll tablespoonfuls of dough into balls, squeezing the dough together if it is crumbly. Arrange 2 inches apart on the prepared pans and press a pecan into the top of each.
Bake, switching the pans halfway through, until the cookies are just set around the edges but the centers are still soft, 12 to 15 minutes. Let cool completely on the pans.
Make the glaze: Whisk the confectioners' sugar, the remaining 2 teaspoons whiskey and 2 teaspoons water in a small bowl until smooth and thick. Gradually stir in up to 1 more teaspoon water to thin if necessary. Drizzle over the cookies; let set 10 to 15 minutes.