Preheat the oven to 375 degrees F (190 degrees C). Line 24 muffin cups with paper liners.

Place sugar and butter in a large bowl; beat with an electric mixer until light and fluffy. Add eggs and vanilla extract and beat until smooth.

Sift 2 cups flour, baking powder, and salt together into another bowl. Toss blueberries with remaining flour.

Beat flour mixture into the creamed butter and sugar on medium speed, alternating with milk, beating batter briefly after each addition. Fold in blueberries. Divide batter among the prepared muffin cups.

Bake in the preheated oven until tops look dry, about 15 minutes.

Whisk powdered sugar, water, lemon juice, and zest together to make a thick but spreadable glaze. Remove cupcakes from the oven and spread 1 tablespoon glaze over each.

Return cupcakes to the oven and continue baking until golden brown, 8 to 10 minutes more. Remove from the pans and cool on wire racks.