The problem is fathers weren't always noted as deceased even if they were but if Ann says married in 1901 that is further evidence he was still alive.
I wonder is there a death for little William Charles? He would only be 10 in 1891 so not likely to be out on his own.
Have you checked grandparents on 1891 census as they often had grandchildren with them.
The 1891 census has the whole family missing! which is odd, apparently though 1891 was when the Suffragette movement had a lot of women refuse to carry out the census, so potentially, James was 'under the thumb' and went along with what Ann said?
Will have a further look into the grandparents in 1891, but the Hills family are very much a brick wall.
Ann and James had a daughter- Charlotte who passed aged 1, then Eliza(my 2x gt grandmother) and a brother...
finding any of them, other than Eliza is proving a challenge.