In my experience I would speculate census accuracy in regards to people being present or missing is still a extremely high %.
Given that one runs across 'visitors' to households on census nights occasionally, maybe 10% of the time or less, in theory the same could be applied to those missing, more or less.
The Harden family already had quite a number of people living in the residence, at least five children, the parents, a relative and a boarder.
The probability another two people were living there and just happen to not be included because of absence is low. A point in favour is, if they were elsewhere the likelihood they would appear in that census somewhere in another residence, or as boarders in another place is high and they do not. If they were at an actual hotel during some weeks of this period the father John Grant claims they were living in the Plumstead area, they may not have been included.
It is wishful thinking that would make the story make more sense but most stories don't make sense and this entire story about Polly Tyree has made about the least logical sense of any I've encountered in over 15 years; which is exactly why it has been so difficult to unravel.
The problem with census returns is the fact that not 100% of the population are recorded.
OK If you are the Smith family living at 2 Jones Street Anytown you are virtually going to be recorded.
What the census form says is record people who were in your household on the night of 31st March, the couple didn't have a fixed address and although the landlady stated they had lived with her it's possible they spent the night somewhere else, or it's possible she was only allowed to have one lodger who she did declare.
My way forward would be to get a copy of the unknown female death certificate to see what the cause of death was, if it was found drowned in the Thames then see if you can find more detailed information about the unknown female burial from the cemetery records, if it says found drowned in the Thames I think you will have found her. She will have been buried in a common grave.