The three 'holes' are the result of the 3 carpels (the female reproductive organ of a flower, consisting of an ovary, a stigma and usually a style) in coconut flowers, and three carpels is typical of the family Arecaceae (Palms). The holes are actually germination pores (germination is the process by which an organism grows from a seed or spore).
Coconut tree is one of the most useful trees in the world, and is often referred to as the "tree of life". It provides food, fuel, cosmetics, folk medicine and building materials, among many other uses. The inflorescence or flowers produce nectar called Coconut Flower Drops that contain medicinal values and can be fermented. This version produces a healthy alcoholic beverage.