That scale is one issue right away. Don't do 1 unit=1 meter for a huge space sim. Doing a 3,000 unit size spaceship makes sense for, say, a level of a first-person shooter set inside the spaceship, but for a large-scale space sim you want *ahem* a larger scale. Depending on what exactly you are doing you might consider 1 unit=1 decameter (10 meters) or even 1 hectameter (100 meters.) Thus a 3 kilometer long spaceship is only 30 units.
That said, you should probably be flexible about that scale over the course of your game. In shots representing a universe all at once you would want a bigger scale, while in shots on a planet's surface you would want a smaller scale. Scale/resize all the objects around the camera and simply change your mental notion of what units mean as appropriate.
You better start thinking about LOD, because managing assets over enormous expanses is the main difficulty in writing a space sim. I would recommend doing stuff like only representing the couple thousand units immediately surrounding the camera with real geometry and using texture stand-ins for everything further away, never moving the camera too far from the origin (move the world around the camera instead,) and the aforementioned changing of scale (resize objects around the camera and change what you think units represent.)
That said, you should probably be flexible about that scale over the course of your game. In shots representing a universe all at once you would want a bigger scale, while in shots on a planet's surface you would want a smaller scale. Scale/resize all the objects around the camera and simply change your mental notion of what units mean as appropriate.
You better start thinking about LOD, because managing assets over enormous expanses is the main difficulty in writing a space sim. I would recommend doing stuff like only representing the couple thousand units immediately surrounding the camera with real geometry and using texture stand-ins for everything further away, never moving the camera too far from the origin (move the world around the camera instead,) and the aforementioned changing of scale (resize objects around the camera and change what you think units represent.)