Hi Megan, I too suspect they are different people, and I think neither may be correct?
There is a lot of mixups of at least 3 different families that I have seen, and no sorry I don't which is right or wrong LOL.
Hamiltons is an area of interest for me, however it's a real rabbit warren with all the John, James and Margarets :D
there is a 3rd possible here: [[Hamilton-4739|John Hamilton (abt.1690-)]]
-- I haven't managed to decide which is which on the John's/James as yet but I started with your Margaret married to James Smellie and have doubts about her parents as you have them..
what I have narrowed down so far is that there are (at least) 3 Margarets born 1724 - 1728 to a John Hamilton, and most trees out there are like the Margaret on your profile and have latched onto the John born to James which may be correct but ... :D. There is also another Margaret born to a Robert Hamilton and Margaret Walker (note the dates below may be christening dates however there is just usually days between birth and christenings in the Scottish OPR's) - all 4 of these are muddled up in the Ancestry Trees I've looked at.
* Margaret b: 16 Feb 1724, Barony, Lanarkshire to Robert Hamilton and Margaret Walker
* Margaret b: 15 Nov 1724 in Renfrew, Renfrewshire to John Hamilton and Margaret Mitchell
* Margaret b: 4 Dec 1726 in Hamilton, Lanarkshire to John Hamilton and Janet Young
* Margaret b: 28 Jul 1728 in Glasgow, Lanarkshire to John and Margaret Millar
I suspect that it's the Margaret born 1724 to John and Margaret Mitchell in Renfrew that would be the one married to James Smellie, firstly because of their marriage location of Renfrewshire (Brides parish) and also the naming convention of their children 1st Daughter Margaret, 2nd son John. There are none of their children named Robert (at least not that I've found) so while there are even more Margarets born to a Robert in the right place I suspect you could rule them out, I only put the one in my list in as there is an Ancestry tree with them linked, likely because of the 1724 date 
I can only find 2 x children born to John Hamilton and Margaret Mitchell (m: 1723) Margaret in 1724 and James in 1727 so perhaps Margaret Mitchell died young and John remarried.. I would love to collaborate as you suggest in the bio however I don't want to change anything that you may have already proven :D
are you working upward from that definite (Smellie) marriage or working from top down trying to sort out the Johns and James'?
The other profile with the John m to Margaret Watson parents of David Hance Hamilton has no sources and again conflicting information as to David's parentage on Ancestry so would not really call a dupe on that, yet anyway :D
