In my main desktop genealogy software I frequently cite the census as a family source, but generally do not attach it to the individuals enumerated. I always note where the census was taken and generically who was enumerated with the head of household, eg, “Town, County, State, wife and 5 children,” or “Town, County, State, widow with 2 children.” If there is something I am trying to sort out with the family, I may transcribe the census.
In another program I use, which handles facts and sources a bit differently, I have the option of adding a census “fact” to an individual (ie, head of household). If the person had different wives in the different census, I can “share” that fact with the head of household and the wife.
Since US census info is generally easy to find, I see little value in transcribing the enumeration. However, if there is something in the entry that makes it difficult to find, such as some bizarre spelling, I will note that.