Hi,
when you use the 'Ctrl' the shape is duplicated which is different from shape copying. But may be you are right that if the shape has a copy protection it's also shouldn't be duplicated. We will revise this behaviour for the next version of the diagramming component and make the diagram honour the Copy protection upon duplication, too.
To prevent the duplication, take a look at this post: http://forum.nevron.com/shwmessage.aspx?ForumID=3&MessageID=2424