How do I hide object in scene editor?

The Layers button in the top-right of the Unity editor window allows you to choose which layers you want to see in the scene view. So you can put your ship in a separate layer and then hide it. You can also 'lock' layers, so they are visible but can't be selected.

You can't really "lock" gameobjects, but you can hide them or prevent editing in the inspector by setting the hideFlags. Watch out since the hideFlags also controls if the object is serialized or not.

The HideFlags is a bitmask, so you can combine them with the binary or "|":

     public enum HideFlags
     {
         HideInHierarchy = 1,
         HideInInspector = 2,
         DontSave = 4,
         NotEditable = 8,
         HideAndDontSave = 13
 }

HideAndDontSave is already a combination of "NotEditable", "DontSave" and "HideInHierarchy"

Rather than specifically disabling mesh renderers, just disable the entire object, or better still, put them all as children of an empty object, and disable that. Then, re-enable it just before testing your scene. Unity does not have a built-in "lock" setting, but there are editor scripts you can download to do it, or you could write your own.