A minimal sample of how to handle ScriptableObject drag and drops into a scene view and onto a given GameObject.

CustomScriptableObjectAssetEditor.cs

//Minimal sample of how to drag a ScriptableObject into a scene
//onto a GameObject in that scene, and have something happen as a result

using UnityEngine;
using UnityEditor;

[CustomEditor(typeof(CustomScriptableObjectAsset))]
public class CustomScriptableObjectAssetEditor : Editor
{

    //Note: Older versions of Unity do not have the index argument
    //So if that gives you errors, just remove it. 
    internal void OnSceneDrag(SceneView sceneView, int index)
    {

        Event e = Event.current;
        //Get the GameObject we're hovering over (if any)
        GameObject go = HandleUtility.PickGameObject(e.mousePosition, false);

        if (e.type == EventType.DragUpdated)
        {
            if (go)
            {
                DragAndDrop.visualMode = DragAndDropVisualMode.Link;
            }
            else
            {
                DragAndDrop.visualMode = DragAndDropVisualMode.Copy;
            }
            e.Use();
        }
        else if (e.type == EventType.DragPerform)
        {
            DragAndDrop.AcceptDrag();
            e.Use();

            //We've let go of the mouse here, so now we can do whatever we want to happen
            //Get the ScriptableObject from the target
            CustomScriptableObjectAsset asset = target as CustomScriptableObjectAsset;
            
            //And now apply ... 
        }
    }
}