It is a reference to some political articles written about America. The articles in question discuss the notion of America being an Empire and whether or not it is in economic, political or cultural decline. Since the Second series of Standalone complex is an allegory for American and Japanese relations during the Cold War in the 1970s, it seems only right to call the USA the American Empire in homage to the the politics of the time. That is that America was declining economically with the Oil Crisis and Japan becoming one of the top economies, whilst still being militarily subservient to the USA.
I believe they discuss it within the special features on some of the series DVDs, but there is also a written piece within the Second GIG boxset that talks about how the Second series is metaphor for the tensions between America and Japan during the Cold War. So to answer your question with a simple answer. No, it is not a snide subtle comment against America, it is more a reference to the politics of the time. Although, I am sure the Japanese would view the USA and its cultural power as being somewhat of an Empire.
Hope that answers your question.
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