How can I get reference of a GoCollapsible Handle after it has been added to a node?
When I search for the handle in the document layer it doesn’t return any handle object.

That’s right–if you added a handle to a node, it is a child of that node, so it won’t appear as a top-level object in any layer.
You need to search the node, perhaps by enumerating the child objects of the node. Or perhaps you can assume it’s the last object in the group (GoGroup.Last). Or perhaps you know which index it is, since GoGroup implements IList (node[5] as GoCollapsibleHandle).