Preheat oven to 350 degrees F (175 degrees C). Line a 12-cup muffin tin with paper liners.
Mix flour, baking soda, and salt together in a bowl.
Heat 5 tablespoons butter and milk together in a saucepan over low heat until butter is melted, 3 to 5 minutes. Remove from heat.
Beat white sugar, eggs, egg yolk, and 1 teaspoon vanilla extract together in a bowl using an electric hand mixer on low until mixture is smooth and thickened. Slowly pour flour mixture into sugar-egg mixture while mixing with the electric mixer until just incorporated. Slowly add butter-milk mixture; beat until just combined. Fold in 1/2 cup shredded coconut. Fill muffin cups with batter.
Bake in the preheated oven until a toothpick inserted in the center of a cupcake comes out clean, about 20 minutes. Cool in the pans for 10 minutes before removing to cool completely on a wire rack.
Beat softened butter and cream cheese together in a bowl using an electric mixer on medium. Gradually beat confectioners' sugar into creamed butter mixture on low until incorporated. Beat in 1/2 teaspoon vanilla extract and lemon zest until smooth and creamy. Spread frosting over cooled cupcakes; sprinkle about 1 teaspoon shredded coconut onto each cupcake.
