ACF is not checking your templates for the use of specific functions for specific fields.
ACF is not checking to see if you’re using shortcodes for specific fields.
ACF has no idea if there is actually a problem or not.
ACF is simply looking at the content on a given page when you load the admin and comparing the content before and after applying wp_kses() to see if they are different.
Altering your code on the site will not change the fact that you have content in your database that will be altered by wp_kses().
The warning is so that you know there is a difference and do something to prevent the altering of your content by wp_kses() before they release the version that will actually alter that content so that you can prevent your site from breaking when that update is released.
