Unless code has been added to explicitly avoid it, the user will be able to interactively add multiple links to any node.
The JGoPort ValidDuplicateLinks property will, if true, disable the ability to make 2 or more links between the same 2 ports, but muliple links to/from one port to/from many other ports is allowed. Similarly, the ValidSelfNode property only controls whether a link can be created from a port to itself.
You shouldn't need to modify properites like ValidDuplicateLinks or ValidSelfLinks when saving or loading XML. These properties should be set when the user interactively creates the links. The XML save and load should simply preserve the values of these properties.