Thanks for all the feedback.
Have you got any marriage certificates of children, to see whether they claimed he had died?
Have you found her death?
I hadn't considered that about the marriage certificates, I'll have to look into it. However, most of their children died young and it looks like the earliest marriage was by the son Lawrence in 1919.
As for Mary's death I believe she died in 1944 and was buried in the same plot as her son Charles who died in 1920 from a war related illness. I haven't found anything to suggest Thomas was buried there too, or in the same cemetery.
I do now wonder if I've mixed up two people. For instance, his uncle Benjamin also had a son called Thomas, born two years later in 1859. And as has been pointed out, the 1888 the age on the marriage bann to Mary Hodgson roughly fits (29), but on the 1891 census his age is actually younger (26)! Why the disparity?
All the children that have been mentioned (Charles, Lawrence, Mabel and Emma) have the mother's maiden down as Hodgson on the GRO website, so it does appear to back up that I've got the right man.
I have a marriage with Mary Hodgson 4th Q 1888 Barnsley, Volume 9C Page 247
I also have a death for Thomas Mallinson 1st Q 1916 (so could have died 1915) Barnsley Volume 9C Page 265, stating birth 1853, age 63 - that bit only being to the best of the informant's knowledge
I have a birth for a Thomas Mallinson 4th Q 1857 Barnsley, Volume 9C Page 113
I also have a Thomas Mallinson turning up on ER pages for addresses in Barnsley 1880s through to 1915: address in 1903 is Freehold land on Eldon St North, Barnsley and in 1915 is a dwelling house at 50 Grafton Street (does this match with the death certificate?)
Stitch
I'd considered this one before, but he has a probate for 1916 where he leaves his effects to his widow Jane Mallinson.
One final thing. Thomas' mother Emma Mallinson lists that she had 9 children on the 1911 census and that 5 of them had died. Though I can actually only find 8 kids, I have the 4 that were still alive at that point, so that suggests Thomas must have been one of those that had died.
So... assuming he died before 1911, but was alive in 1902 to father another child (called John Patrick), that at least gives me a window to work with.
Again, thanks for everyone's help.