Custom Post Type vs Shortcode: Which one is more performant?

If the posts with tables are part of “normal” blogging flow and appear with rest of the posts, there is probably little reason to separate them out into CPT. Shortcode bit is irrelevant, you’ll have to deal with tables regardless of native or custom post type.

The use cases for CPTs loosely start for content that no longer belongs in stream of blog posts (or arbitrary purpose pages).