There is nothing that I know of in ACF that stores any information about the WP table prefix. ACF uses WP function the get and set values. The ACF functions are simply wrappers for WP functions and what anyone can do using those functions.
On a side note, altering the table prefix does nothing to improve security of a site: https://www.wordfence.com/blog/2016/12/wordpress-table-prefix/
