Hi,
Yes, that is definitely the cause then. Since you added FTP credentials, I have implemented this custom code to the functions.php in your theme directory. I assumed from the ACF configuration that the field name containing the items is named ‘content_elements’, so I have added that to the code.
Then I re-indexed everything, and the keyword count went up to 13k, but I am not sure if the tables are indexed, you might have to test that. It is also possible that I have not added the correct field, in that case, please edit the code, and add it to the $field_names variable, then re-index everything. It might do the trick.