Sorry for my slow response. It was a bit of a crazy week.
There is a ship limit, which is 2000. There is also a legacy off by one error that allows for 2001 to be created.
Ship management is a big part of the game. If you have some ships you no longer need, you can use a regular: DELETE FROM my_ships WHERE <etc>;
You will find that as planets run out of fuel, or if you have enough resources already, it makes sense to kill of miners and start sending new ships out elsewhere.
Hope that helps!