There is a marriage between Thomas Nixon and Agnes Meek in Ballymena on 12.7.1892, but on that marriage certificate Thomas’s father was named Thomas, not Joseph. So, if that’s correct, that cannot be the Thomas born to Joseph Nixon and Ellen Larkin. You can view the 1892 marriage on this site, and decide for yourself:
https://churchrecords.irishgenealogy.ie/churchrecords/
I note what you say about the information on Thomas’s death certificate in Glasgow, but it doesn’t reconcile with the marriage certificate. One of them must be wrong. Usually the information on a marriage certificate is more reliable since it came from someone with first hand knowledge, whereas on a death certificate the information must inevitably be second or third hand, with the informant often not knowing that much about the deceased’s parents. Mistakes on death certificates are quite common.
I can see 3 children born in Ireland to the Nixon/Meek marriage: Ellen 24.6.1894, John 23.6.1896 & Mary 9.4.1899.
The family’s move to Scotland was before April 1901 since they are in the Scottish census at 27 Gilmour St, Govan.
I had a look for a Thomas Nixon birth to a Thomas Nixon father but didn’t find one.
I can confirm that there was a marriage between John Meek and Mary Kernohan, registered in Ballymena on 17.9.1866. (He is indexed incorrectly as Meck).
You can view the original certificate on-line on the GRONI website, using the “search registrations” option:
https://geni.nidirect.gov.uk
You will need to open an account and buy some credits. It costs £2.50 (sterling) to a view a certificate.
This is probably the Meek family in 1901:
http://www.census.nationalarchives.ie/pages/1901/Antrim/Ahoghill/Lisnafillon/924151/
And in 1911:
http://www.census.nationalarchives.ie/pages/1911/Antrim/Ahoghill/Lisnafillon/115308/
The Meek family were Moravian. They are probably buried in the Moravian burying ground in Gracehill near Ballymena. There’s a Moravian church in Gracehill with records that start in 1749. The records are not on-line anywhere but there are copies in PRONI (the public record office) in Belfast. A personal visit is required to view them. Here’s what the records contain:
Diaries which record baptisms, marriages and deaths and the movement of members, 1750-1899; baptisms, 1749-1986; marriages, 1758-1862; burials, 1766-1987; Elders’ Conference minutes, 1755-1892; Congregational Committee minutes, 1788-1927; Congregational Council minutes, 1790-95 and 1833-93; Lot Conference minutes, 1755-91; register of members, with an index, 1755-91; register of pupils and teachers at Gracehill Academy, 1805-83; reviews of the years’ activities, including details of births, marriages and deaths, 1863-91 etc.; printed history, 1984.