Local JSON files increase the speed of your site by loading field groups and field definitions from the file instead of making database query.
The local JSON files will not effect the displaying of the content of those fields that is saved to a post whether they are shown with shortcodes or using functions like get_field() or the_field() in PHP code. The same number of db queries will be done in either case. The only difference is that there are a couple of extra layers of PHP processing that needs to be done. The extra PHP code/function calls should not create a noticeable difference in performance. I can’t give you any testing data, but it would probably takes many thousands of shortcode calls to effect the load time of a single page.
