Dear Pat
Stanley seems to have borne his mother's surname, as many illegitimate children do, but the fact that you can't find his birth entry under that name suggests to me that he was given a different name at birth - maybe Isabella gave him his father's surname. She may have done this in innocence, not realising that she wasn't supposed to.
I spent 20 years looking for my great great grandfather Charles Winchester Giesen, only to find that his name at birth was Charles Winchester Green Culling. It's odd that Stanley isn't with Isabella in the 1901 census. Have you looked at the neighbours' households or any relatives, who perhaps lived at some distance? Perhaps he was sent away to stay with family to avoid letting the neighbours know what had happened.