Leaving one's ship beached or anchored unattended for several days in Valheim is roughly like leaving one's car parked on the street downtown in a major American city unattended for a similar period of time.

Unless one is exceptionally lucky, it will not be there when one returns. One may take measures to protect the ship. A workbench will keep mobs from spawning in the immediate area but do nothing to prevent storms or wandering mobs. If one's ship is destroyed, a workbench will keep the component parts from de-spawning.

Except for deer and fish all the creatures in Valheim seem to delight in destroying ships.