First, dont step on the deck, never, it resets the ~21 dayish decay timer. If you think, someone else messing with you and keep boarding that ship once in 1-2 weeks, then try to build a wall around the ship to prevent that action/trolling. After around 2-3 weeks the ship will despawn if none touches it.
But, of course, first check your server settings.
- If youre on official, the decay timer is around 2-3 weeks.
- If youre on unofficial, then there is a chance, that decay system is disabled or the timer is modified. Ask the owner of the server about this, or if she/he is an active player, ask him to help destroy your ship with console commands (probably there is command for deleting something, or a command for adding exiting ships to your company, so you can destroy it by yourself).
- If youre playing in local host, then the host probably can use those console commands too.