A fun speculation, but I think I have too much of a clouding bias with the 6 extra holes, and certainly my "better" is another man's "worse".... but here's a few thoughts:
1. Golf may have remained a more provincial, "backyard" game, with less commercial professionalism and standardization.
2. Because "12," a dozen, is such an embedded cultural number beyond golf (whereas 18 instantly brings the mind to golf), I speculate that courses/operators would have felt freer to distinguish themselves by varying the number of holes.
3. At a 12 Standard though, GCA/length-par may have been divided one of two general ways: either four of each (3, 4, 5) or ten "4s", one 3 and one 5.
4. It's my 18 bias speaking, but I do think a shorter number of holes would have made for more audacious, memorable architecture intentions with each of a shorter number. We seem to accept, even on beloved 18 hole courses, a hole or two that is plain or seen everywhere; I think the tolerance for this would be less and the notion to make each hole unique, greater.
5. With the 1/3rd less acreage needed, we may have seen more "shore/links" courses in America and/or the reduction in poor inland properties (or their unfriendliest sections) should early GCA have otherwise developed as it did. One imperfect, anecdotal example is the nominal first/early/remaining US club, St. Andrews...they started at a makeshift 3 holes across from Reid's home in Yonkers, moved 300 yards northwest to a plotted course of 6 holes in Shonnard's meadow...both of those are on pretty flat hilltop land, but when they were compelled to go 1/3rd of a mile north to the "Apple Tree" 9-hole course, they were on a ski slope of that hilly section of Yonkers, a thing which didn't stop as they chose hilly sites in the next two moves...the Odell Farm 9hole course of the that "first" disputed National amateur, and the current course in 1897, which had it stayed at 9, and on that site, may have developed over the "flats" which encompass holes 4 - 8 and 14-18 and NOT the mounatineering side of the other holes.
cheers vk