Bug Not solved. Sub asset become main asset. U 5.3.3p2. Only way to do it is to set
subAsset.HideFlags=HideFlags.HideInHierachy before add. Then you out of Debugging option. Shame on Unity.

Update: It does seem to work if I change the name of the Scriptable Object before adding it. Yay!

Definitely still broken as of 5.3.4f1. When I try adding a Scriptable Object to an asset, the parent-child relationship seems to be reversed, and I get the following error:

NullReferenceException: SerializedObject of SerializedProperty has been Disposed.

Code:

Object child = ScriptableObject.CreateInstance(type);

AssetDatabase.AddObjectToAsset(child, parentAsset);

This issue appears to be flagged as "resolved", since you can not longer vote on it ... but it's still not functioning as expected.

AssetDatabase.AddObjectToAsset (subObj, mainAsset)

When mainAsset is a ScriptableObject, the call results in a new generic object being created with both the mainAsset and subObj as children. Instead the subObj should become a child of the mainAsset. That's it.

This still seems to be an issue. Is there any update?

As of Unity 4.3.1 you can call AssetDatabase.AddObjectToAsset(sub, main), but you will get a new main asset (of type UnityEngine.Object) with two children -- sub and main.

This would clean up my plugin tremendously. Currently, I have to create a separate "main asset" and put all the children in a separate asset.