Looks like David and Mary married between 1891 and 1901, if you decide to try for the marriage certificate from Carmarthen Register Office.
1891 at Brondeg Cottage, Broadley, St Ishmael
David Thomas Head age 36 Collier born Carmarthenshire
Rachel Thomas Wife age 37 born Llandefaelog
John Thomas Son age 12 Scholar
Eliza Thomas Daur age 10 Scholar
Lewis Thomas Son age 8 Scholar
Maria Thomas Daur age 6 Scholar
Mary Thomas Daur age 4 Scholar
Henry Thomas Son age 3
William Thomas Son age 1
May help you track down the parent(s) of John Thomas!
Added:-
... So far I think only Mary had children from the 5/6 kids they had.
so Rachel had the children, and David probably married Mary sometime around 1892-3 and definitely before 1901. Check how long they had been married on 1911 census to help narrow down the marriages.