Storing complex GameObject structure

Well, my first answer was "Yes"

For a couple of reasons:

1. I read your question incorrectly: "Strong complex GameObject structure" and totally missed the "how" in "how should I store" and so now it's a yes/no question.

2. I was actually having a very bad day, and I wanted a relief in the form of a laugh.

For the answer:

It all depends on your needs. It would have been more helpful if you provided more details as to who's accessing the points, what part of the game object hierarchy you're interested in, why have a "DestinationPoints" instead of the points just being children to the ProjectionSurface? etc.

Here's one way to store them (based on the current hierarchy you posted):

 public class ProjectionSurface : MonoBehaviour
 {
    public List<GameObject> destPoints = new List<GameObject>();
    private void Awake()
    {
        PopulatePoints();
    }
 
    private void PopulatePoints()
    {
        destPoints.Clear();
        foreach(Transform point in transform.GetChild(0))
            destPoints.Add(point.gameObject);
    }
 }

But this is not safe, it's depending on the fact that "DestinationPoints" is the first child - so you might be better of writing an extension method for Transform that gets a child by name, like:

 public static class TransformExtensions
 {
 public static Transform GetChild(this Transform inside, string wanted, bool recursive = false)
 {
     foreach (Transform child in inside) {
         if (child.name == wanted) return child;
         if (recursive) {
             var within = GetChild(child, wanted, true);
             if (within) return within;
         }
     }
     return null;
 }
 }

And so now the Populate method becomes:

    private void PopulatePoints()
    {
        destPoints.Clear();
        foreach(Transform point in transform.GetChild("DestinationPoints"))
            destPoints.Add(point.gameObject);
    }

But now you might have trouble if you rename the DestinationPoints game object...

Safest solution (what I would go for) would be to store a reference to the DestinationPoints GO instead of having to look for it:

 public class ProjectionSurface : MonoBehaviour
 {
    public List<GameObject> destPoints = new List<GameObject>();
    public GameObject destinationPointsGO; // set via inspector

    private void Awake()
    {
        PopulatePoints();
    }
 
    private void PopulatePoints()
    {
        destPoints.Clear();
        foreach(Transform point in destinationPointsGO.transform)
            destPoints.Add(point.gameObject);
    }
 }

Now you can easily access your points via myProjSurface.destPoints[index]...

Did that help? if not just ask...