I was correct in my theory that the girls were born in Jamaica during Thomas's time there, and that their mother was of coloured ancestry. The baptism entry of the first daughter of Thomas Hughan and Margaret Hook ( below) reads "Baptisms in Kingston 1793. Jane, the daughter of Margaret Hook, a quadroon woman, by Thomas Hughan, was born 14th April, 1792, and baptised 23rd June, 1793."
The following year, when younger daughter Margaret Hughan was baptised, Margaret Hook was described in the church record as being "a free mulatto woman".
By definition, a 'mulatto' was an individual who had one black parent and one white parent. A 'quadroon' was the child of a mulatto parent and a white parent.
Margaret Hook's father was a white merchant, Duncan Hook, whose relationship with a mulatto woman, Elizabeth Duncan, resulted in a family of three daughters and four sons. Duncan had to have a special Act of Assembly passed to give his mistress and their children the same legal status as English subjects in Jamaica. It was granted on 21st of December, 1776:
"An Act to entitle Elizabeth Duncan, of the parish of St Elizabeth, in the county of Cornwall, and island of Jamaica, a free mulatto woman, and Elizabeth Hook, Mary Hook, Margaret Hook, Henry Hook, William Hook, Thomas Hook, and John Hook, the reputed children of Duncan Hook, merchant, by the said Elizabeth Duncan, to the same rights and privileges with English subjects, under certain restrictions."