If we take the book at face value, Anne Hughes was around twenty when she married and twenty-two or twenty-three when she began writing in ‘her boke’. At the outset, she tells us how long she’s been married and later tells us she’s the same age, 24, as her childhood friend, Lady Susan, whose birthday she shares. She stops writing just before the birth of her first child and never resumes. We must hope the reason was the one she gave, that she will be too busy to write in the future.
Anne appears to have been the daughter of parents who knew how to run a farm and its domestic support systems. She knows how to look after livestock, to harvest crops and butcher animals and shares in these tasks. She also knows how to sew, cook and preserve and to deal with servants with confidence. Although she never refers to her father and only ever to her mother, it is often to tell us about something she’s been taught by her. We learn that her mother has died and assume her father has too. There is no mention of a brother or sister which is perhaps unusual. Cousins are mentioned but it's not clear if they are on her side of the family or John's.
If you wanted to choose a difficult name to trace in an area in the proximity of Wales, Hughes would be a good choice. There are contenders in the records, but deciding which is the right Anne and what her maiden name was will depend on a sufficiently large number of other types of record to make for a convincing case.