Yes. WhereUsed scans post meta (even post meta created by ACF). There is a caveat to that. ACF may associate a value of a custom field to another post using a post ID. At the moment, WhereUsed does not know that the value (a number) is indeed a post ID. It could be a count or something else. The same goes for a custom field that is added by PHP code. You can make your custom field fully compatible with WhereUsed by using this hook.