The IDs you are mentioning are an implementation detail of the GraphML format and are no longer available once the graph has been read from GraphML.
If you want to or need to identify elements by ID in the yEd application, you need to define a custom property for this purpose. Doing so has the additional benefit that yEd's structure view, "Edit" -> "Find", and "Tools" -> "Select Elements" all support custom properties for quick navigation (and selection).