Currently, only defined properties are serialized within the NavigationToolReader / NavigationToolWriter. Using the MITK serialization functionality for DataNodes to save all properties of the DataNode associated with the NavigationTool will allow custom properties to be saved.
In this context, Point3D and Vector3D properties can also be saved directly without having them to be converted to a string first.
See also conversation on mailing list: https://sourceforge.net/p/mitk/mailman/message/36301206/