Ok, I've been checking the various Jenkin(s) wills from Llanfihangel ar Arth that are on the NLW website.
There's one from 1740, written 20 April 1738, for a Griffith Jenkins who makes bequests to various nephews & nieces including John Jenkin of Nantylloch & John's brother Thomas. There's also Griffith's brother Thomas Jenkin whose children were David Thomas, Isaac Thomas, Sarah Thomas, Rachel Thomas, Mary Thomas, Hannah Thomas, Margaret Thomas, so looks like use of patronymics.
There's a will from 1720 of a John Jenkin which looks to be helpful. At the time of writing in 1720 he was occupying Nantylloch. He bequeathed his holdings in Cardiganshire to his eldest son John, Nantylloch Ucha & Issa went to his wife Mary and after her death to son John. To his youngest son Thomas he left 2 bullocks, a bushel of corn, & half his books. The rest of the books went to John. There was a legacy for nephew James William. The rest of the estate was left to his wife Mary & daughter Eleanor who were the executrixes. This might suggest that Thomas was too young to be the executor.
So it seems that John Jenkin may have died between 1740 & 1770 when Thomas' will was written.