Don't really think that family group were Dissenters as all their children were christened in the CoS church. I think - as you suggest - that the registers were deficient OR just as possible, they were married OK but refused to pay to have their names entered. That apparently was very common practice around that period as the church /govenrment were (once again) trying to raise money by taxing necessary items and their subjects were registering their displeasure by not paying up. I may say, that I can't locate his mother's second marriage either to John Dunn between 1747 and 1750, but again the subsequent children all appear in the register!
Enid