I didn’t notice any performance issues or a flash of unstyled html, but it probably depends on what your JS is doing. Mine was for a slider, and I believe I had all the slides but the first hidden via CSS until the script was fully loaded. So you may have to do something like that, style the element for before the script loads, then for after. Many scripts will add a class to the relevant element once the script is loaded, making it pretty easy to manage.
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users