Looking at William and Honour, they were married on 7 Jan 1765 at Horton. Honour's maiden name was Maller.
Nicholas' age at death places his birth at 1761, that is, before the marriage. He was, therefore, at that stage, illegitimate. I can't find a baptism for him either as Jones or Maller, so perhaps he wasn't baptised in Horton (or elsewhere) or the record hasn't survived. If William was his father, then he would be regarded as legitimate on the marriage, else if Honour was his mother, then he was William's stepson and took his name.
BTW William and Honour had another child, Robert, baptised 13 Dec 1767 at buried 14 Aug 1768 at Horton :(
The best I can suggest is looking to see what the Records Office may have. There may may be a bastardy order, or if William was his stepfather, a mention in William's Will, if there was one.
Tracking Richard and Ann may also provide a clue.