Well, the difference is that when you delete an object in the scene, it is removed from the scene, that is, it is no longer among the children. While when it is simply set to invisible, it still remains in the scene data structure and can be used in calculations, for example, to rotate another object towards it.
But yes for rendering at the end there is no difference, both ways are to omit this object from the picture.
, , , . , , , , , , , . , , , , - ( , , - ).
, , , , , , three.js