Obviously as Markdown is HTML-oriented, you can still write superscript/subscript with <sup> and <sub>. So this isn’t a loss. There are some proposed extensions to support some of these (e.g. https://talk.commonmark.org/t/why-there-is-no-syntax-for-subscript-and-supscript/586), but nothing we have to actually wait on. For small caps, you simply get a pair of tokens HtmlTag("<span style=\"font-variant: small-caps;\">") and HtmlTag("</span>"), with Markdown in between, that you can recognise instead of escaping it as <span> etc.
Would these titles benefit from Pandoc-like math syntax in $ signs? Biology I’m guessing no, but chemists might like a “pass this straight through to LaTeX please” where they get to \usepackage{mhchem} and not get bogged down in subscript soup. That’s not what math is, but same kind of thing at least.