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Margaret may have died before Duncan married so he may not have been in a position to take care of James so maybe a older sibling or his mother may have looked after him
Have you traced all of Duncan's siblings to see if any of them emigrated to Canada and have a son James who would fit

The marriage of a Thomas I found on Ancestry but this doesn't appear to be your Thomas but possibly a nephew from a later reply from Monica

In Scotland females legally don't lose their maiden name and on many legal documents notably wills you will find them addressed as Jane Smith or Watt Smith being her married name and Watt being the maiden name also in the past a possible explanation for widow's using their maiden name was the part in the wedding vows (until death do us part) there was a death so no longer married
So Agnes using her maiden name was common in those times

Another thing I have learned is that sometimes women/men have stated  the spouse dead if they had seperated or were abandoned less shameful to be widowed in those days
When did Jane marry John Potts as couldn't see a marriage wondering if they didn't marry because one of them wasn't free to marry

Finally if Thomas snr was deceased/disappeared at the time of Isabella death who was the father of Thomas jnr

Also possibly a coincidence but there is a marriage record of a Thomas Menagh with a father Simon in Tyrone Ireland in 1865 could your ancestor have abandoned his wife and child and returned to Ireland

There's a death of a Catherine Cameron nee MacLeod in Contin in 1860 mother's maiden name Fraser I notice on Ancestry if I have the right family Malcolm is with his daughter Catherine but not his wife the address is Balblair in 1861 census

Have you tried the burial records Deacsed online may have them There's also local MI book or Find a grave his burial maybe noted somewhere