My G grandfather had brothers named Patrick and James. It could be possible they were recurring family names, but, of course, they are common names. As are James and Mary.
I'm not sure where Mary Clarke or James Nugent were born exactly. They both definitely lived in Rathcore, Co. Meath, prob. since at least 1826. I can almost imagine someone putting down "Johnstown" though since it is so close.
It could definitely be possible that John Nugent, my GG grandfather, had other brothers. i am not sure what happened to his brother Thomas or his uncle Thomas Clarke, only that he won the case.
I am not actually sure where John was born precisely either. The first reference to James taking lease is 1826. According to his reported age at death (not always correct), John would have been born in about 1823. He was said to be the eldest son of James, in a newspaper announcement of the wedding.
If that was the case, it perhaps seems odd that he did not marry first, but I suppose it is still possible. Sons sometimes married out of order. It could also be that the families were more distantly related, or not related at all.
But I don't think the early parish records survive for Rathcore, although I haven't been able to find that out definitely. it could be that they survive locally, within the parish.
What I would recommend you do, is try to find newspaper announcements for the weddings of James and Patrick. One of these may possibly give some further clues, such as the order of birth, whether their father was alive or not, where he was from.
The only other approach I can think of is DNA, if you have been tested. But it may not necessarily be foolproof at that many generations, as sometimes it gets shuffled out.
Edit: John was actually living on the 1901 census.