Hello, I''m thinking about creating a simple multi-player space game with a persistent universe. But I''m stuck with this question: The players being ship pilots, what happens to the ship when the player leaves? Should it dissapear, should it enter a worm-hole, or what? What would be the best solution? Thanks.

You should probably have some sort of "spaceports" where players can safely leave their ships.
If the player quits while flying in space the ship could stay in the world for some time and then fade away. That way you can be sure that players won´t quit when they are losing a fight to save their ship (assuming you´re including combat in your game).
You could also have upgrades that make quitting easier&safer: autopilot, autodefense-system, faster way to get to a spaceport etc.