Scattered perforations in a shell are likely made by boring sponges. These sponges partially acid-digest living and dead shells and invade them as a living space.Many mollusks prey on other species of shells by means of drilling. This means that they use specialized mouth parts and enzymes to excavate a circular hole through the shell and then insert their proboscis to eat the soft body parts of the clam or other shell.
Sometimes octopi also drill holes in shells to get to the tasty animal inside. This may not be the case here. The shell was only about one and a half wide.
The plant was attached to the shell when found. Plants can sink their roots into shells and create holes.