Do occlusion culling. Do not render/update the objects that are not visible.
For example the inside when you are on the outside of the ship (and vice versa) isn't visible so shouldn't be rendered/updated.
Also, if you are on the inside, only render the decks/objects that you can actually see.
Google a bit for different occlusion culling algorithms.
There is no magic bullet for this so compaire different solutions and pick the best for your situation.
Also ask yourself if you really have to move everything at any time. There is a reason you cannot do that in most (AAA) games.