Currently, the best "native" small caps syntax is [Small caps]{.smallcaps}.

By "native syntax", it means a more markdown-ish syntax, such as ^^Small caps^^ or ****Small caps****.

c.f. pandoc-discuss/Small caps syntax possibilities where @jgm said

I think that ^^..^^ is the best of the options you've
mentioned, but I'm still reluctant and would need to
think more about it.