I think there might be a misunderstanding here. Section 4. Advanced Concepts II: Extending GraphML in the GraphML Primer provides examples that illustrate how to add custom extensions to GraphML. (In other words, this section illustrates the general approach for extending GraphML.)
This section may not be understood as a specification for links and SVG data.
That said, yEd does support (hyper)links for nodes. To add a link to a node, select the node in question in yEd's editor tab and enter the corresponding URL in the "URL" field in the "Data" section of the node's properties.
Again, yEd supports links as well as SVG data. It just represents the corresponding data in a more sensible manner than the examples from section 4 in the GraphML Primer.
In short, yEd does support all four of your requirements.