I use Core Data to store large amounts of 3D vector data. I solved your problem in the following way:
I have a "Vector3D" entity that you can think of as an "end point" in your model. My Vector3D entity has x,y,z attributes.
I have a "Vector3DReference" entity.
Vector3D has a "to many" relationship to Vector3DReference which has a "to one" relationship to Vector3D. I can ask any Vector3D for all of its references, and I can as a reference for its Vector3D.
Vector3DReference is abstract. I have derived Vector3DReference for all of the cases where I have other entities with relationships to Vector3DReference. For example, I have a Billboard entity that has a "to one" relationship to BillboardAnchorVector3DReference which has a reciprocal "to one" relationship back to Billboard.
It is common in 3D systems to have a large collection or database of points/vectors and then reference the points/vectors for index or ID. E.g. consider multiple triangles that all share a vertex. When the vertex changes, all of the triangles that share the vertex are updated. Sharing vertex data also reduces the storage required vs. lots of copies of the vertex.
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