Sorry, I did read your question before I got first cup of coffein drink this morning :) Please ignore the part about FAQ and attribute ID (in your case, the <Object> element is inside <Signature> element and it has an "implicit" DTD from xmlsec library itself).
Now back to your question. We have something like this: <Root xmlns="http://examples.com";> <Object>Test</Object> </Root> According to the spec [1] , the non-default namespace node is rendered only if it is in the XPath node-set. In our case, the XPath expression selects *only* <Object/> node itself and none of its namespaces or attributes nodes. Thus I think that xmlsec/libxml do the right thing by returning <Object></Object> after c14n. But as usual with XPath/C14N questions you might want to get a second opinion on this.
Aleksey
[1] http://www.w3.org/TR/2001/REC-xml-c14n-20010315#ProcessingModel
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