BUG: Added missing node references update to scene->AddNode methods

Fixes http://na-mic.org/Mantis/view.php?id=3539.

Problem was that node references were not updated in the scene when
node->SetScene(scene) was called for the node before scene->AddNode(node).

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22788 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Improve readability of vtkMRMLScene::AddReferencedNodeID method

This commit does not introduced any functional change, it just makes
the code cleaner.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22789 3bd1e089-480b-0410-8dfb-8563597acbee