You are correct, I completely agree. There’s nothing deprecated about LaTeX.
What I meant, is that between when pandoc was first created in 2006, and now, it’s much more likely that someone who is using this conversion would know how to write some CSS than some LaTeX to tweak the output format. That is what I meant by deprecated: Today, I would expect it is more likely to find a user that can cobble together some CSS to change attributes than some LaTeX, and so I think a more pertinent tool to convert from Markdown to PDF would expose styling as CSS. But you’re right that it’s just my opinion.
Also I did not know that pandoc allowed using different PDF engines. I just looked it up and it seems Weasyprint is an open source engine that uses HTML/CSS as an intermediate rendering format. That could be a good option to use.