Hi, Lily
I don't know which reference source you consulted for the 1861 census, but in the 3 months since I started researching my family history one thing I have realised is that there are an awful lot of errors in transcriptions.
I have looked at the 1861 information on 'Ancestry.Co.uk' and just as you say the transcription lists Henry as being Jonathan & Hannah's son. However, if you consult the scanned image of the original census it becomes obvious that family groups are listed under one schedule number, and any other families or individuals (such as lodgers) living at that address under separate schedule numbers.
Thus J. & H. and their offspring are listed under schedule 6, Esther and her offspring are listed under schedule 7. Another example - Further along Cross Street, Bradley, the Slater family are listed under schedule 10 and their lodger George Gibson is listed under schedule 11
Given time I will expand my tree further (I have some potential names going back into the 18th century), but for the moment I'm fairly confident that I've got it back as far as Jonathan & Hannah.
Regards
John