I know that webMethods 6.5 sp3 provides and additional input variable “generateNilTags” for “pub.xml:documentToXMLString”, which can be used to achieve your requirement.
In 6.1 this option is not available, in this case you need to do this manually. It might be worth to check if there is any fix available.
But if I assign empty string, it would not result with the attribute xsi:nillable=true, instead it would result in self ending element for the variables as below…