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The census is all about gathering information. Sure, the stated purpose is to provide information for congressional districts and consequently ferderal funding, but the data is used for so very much more. The Census is used by thousands of researchers not affiliated with the government. Anyone can download Census data. (However, the public isn't allowed to see any data that might compromise someone's privacy. All the data is aggregated to some extent.)
Not including information about gays leaves a huge blindspot in our knowledge of the American public. If I were more conspiratorily-minded, I'd think that this is a deliberate attempt to disenfranchise gays by ignoring them. However, the simplest explanation is usually the correct one, and therefore I'm sure that the Census people are just covering their wimpy asses and they don't have the balls to stand up to the feds in charge and demand that this information is VITAL for research and public policy and must be collected.