Preheat oven to 325 degrees. Whisk together flour, baking powder, and salt. In another bowl, beat butter, sugar, and vanilla-bean seeds on medium until pale and fluffy, 4 minutes. Mix in egg and vanilla extract. With mixer on low, gradually beat in flour mixture. Bring dough together with hands. Flatten into a disk and wrap in plastic. Chill 30 minutes.
Roll out dough 1/4 inch thick on a lightly floured surface. Cut out shapes with egg-shaped cutters (we used 1- to 3-inch-long ones); reroll and cut scraps. Arrange on parchment-lined baking sheets. Chill 15 minutes.
For each color, place an egg yolk in a bowl. Add 1 drop food coloring; stir to combine. Add water a little at a time to achieve a paler shade, if desired. Brush over tops of egg shapes. Bake until edges turn golden, about 13 minutes for 1-inch shapes; up to 17 minutes for 3-inch shapes. Let cool on sheets on wire racks.