When JSON fits
JSON is a good fit for structured data: navigation links, footer columns, site config. It is not a good fit for long prose.
When Markdown fits
Markdown is a good fit for pages, posts, and anything with paragraphs and headings. It is not a good fit for nested menus or config.
Mixing both
A SvelteKit project can use both:
src/lib/data/*.jsonfor config and navigation.src/content/*/*.mdfor pages and posts.
Both are readable without a build step. Both can be edited by a CMS.
Summary
Use JSON for structure and Markdown for prose. Do not force one format to do both jobs.