A woman's husband was considered to be the legal father of her children, so it's not surprising for him to be listed on the birth certificate even if he wasn't around.
Looking closely at the Louth Workhouse records might be the way to track things. When is she first listed as "deserted", is there any ever mention of her husband returning or being in there with her, etc. When is the son with no father listed born? (is he "Charles Emerson Standley" in 1895?)
http://boards.tiscali.ancestry.co.uk/thread.aspx?mv=flat&m=640&p=surnames.snowden - a thread here mentions another woman, Emma Humphreys, who he never married but had children with.
In this case is he the one in Louth aged 30 b. "Stone, Stafford", "wife" Emma b. Wales, while Ann is in the workhouse?
He has at least three children with her (
http://pilot.familysearch.org/recordsearch/start.html, baptised as "Stanley"), while Ann seems to be baptising some of her children with no father's name (Albert in 1881, Bertram in 1883, also Charles in 1895). Do you have full records of these? - if this is indeed the same man, he's damn cheeky, because he's christening children with Emma while Ann's christening her children at the same church, sometimes only weeks apart.
I think by 1901 Emma, along with some of her children, is in West Derby. No sign of Henry with them. They use the name Stanley. I don't have access to the 1891 but knowing where both Ann and Emma were at the time would help with tracing Henry George.
