Yes, these James Wilson's are very confusing. But you are able to track them.
I'm not sure who the James Wilson, born 1847 is on the 1861 census, but the parents in this census are definitely James Wilson (born 1818 Lanark) and Agnes Morton. Maybe he died, and they named a subsequent son James (a common practice)? Or maybe he is an illegitimate grandson? James Wilson, born 18 Mar 1867 at Ford Bank is the son of James Wilson and Agnes Morton. This is supported by his marriage to Mary Elizabeth "Lizzie" Carruthers and his death certificate in 1938. And while the 1881, 1891, 1901 and 1911 censuses support his birth date, he is not present on the 1871 with James and Agnes (hence, why the illegitimate grandson theory might be plausible). James and Lizze had a least 6 children, to include Colin Carruthers Wilson, Frederick George Wilson, Bertha Agnes Wilson, Gladys Audrey Wilson, James Townsend Wilson, and Grace Margaret Wilson.
James Henry Wilson, born 01 Apr 1878 at Main River, is the son of James Henry Wilson (born 1852 in Kouchiboucquac) and Mary Jane Flanagan. This is supported by his marriage in 1901 to Mina Roberts (who is actually Wilhemina "Mina" Isabella "Bella" Cail - daughter of George Roberts and Mary Ann/Moriah Cail - I believe she was illegitimate), as well as his subsequent marriage in 1952 to Mary Rita Melanson. And there is a late registration of birth at the PANB that also supports this, along with the census records. James and Mina have at least 10 children. The marriage of his parents James Wilson and Mary Jane Flanagan on the 27 Jul 1878 does not list either parties parents. There is an 1861 and 1871 census in Richibucto with Robert and Ellen Wilson, and son James born about 1850 that may be likely suspects. I haven't been able to prove it out though.
Then there is a James Henry Wilson born about 1869 at Harcourt. His parents are William Henry Wilson and Agnes Ward. He can be found on the 1871 and 1881 census with his parents, but I cannot find him after that.
And then there is another James Henry Wilson, born 15 Apr 1877, son of Alexander Wilson and Mary Jane Quinlan. His baptism can be found in the Acadia Drouin records at Ancestry, but from what I can tell he dies at age 4 in Brooklyn, New York.
Hope all those details help alleviate some of the confusion.