Births in 1790 mean that the parents were probably born between 1760 and 1770. There are certainly Nathans of this period born in Maxwells Walls and in Carnmoney. In Shankill at the same time as Nathan McIlhaggy there was also a James McIlhaggey (spelled slightly differently). He and his wife Sarah had a son William in 1792. Two other Jameses were born in Islandmagee in 1755 and 1788. Finally in the 18th Century a John McIlhago was born in 1788 to a James McIlhago. This is known because he emigrated to the USA and his death is recorded there.
The above facts raise a number of possibilities. We have both a Nathan McIlhaggy - Sarah marriage and a James McIlhaggey - Sarah marriage, Nathan having a daughter in 1790 and James having a son in 1792, both in Shankill, Belfast. Were there two brothers, Nathan and James, who both married a Sarah? Or did Nathan die after Margaret was born and did Sarah then marry his brother James? Incidentally the Nathan in Carnmoney was born about 1758 so is of the right age to be the Shankill Nathan, but we know that he married Betty Burney and had a number of children, none of whom as far as we know was a Margaret.
There is also an 'unattached' Nathaniel who ceased to farm in Islandmagee in 1770, so may have been born as early as 1720. He, based on his probable age, also is somewhat unlikely to be identified with Shankill. The Maxwell Walls' Nathaniels are all too late to be considered as being the Shankill Nathan, though of course Nathan of Shankill may be their ancestor, a link we are at present unable to make for lack of evidence. So, despite a fair number of Nathans and Nathaniels in the 18th Century - clearly it was a popular name - we are no nearer to identifying the Shankill family.
Without a surname, I cannot speculate about Sarah. And what of Margaret? There is a Margaret (of unknown birth year) who married James McHag(g)o and had a son James in 1828. A 1790 birth for this Margaret would fit. There is also a Margaret McElhaga who died in 1845 in Ballymena. Again the date fits, but I have to say that both these Margarets seem to offer only very remote chances of finding a real identification. O dear! Let's hope for some new information which will throw more light.