wp-config.php includes scope for settings for “DB_CHARSET” and DB_COLLATE. Are those settings operative? How do they correspond to the your actual database settings.
If the config settings are operative, it might you might try it with them commented out.
Edit:
On reflection/research, I would set the db_charset and db_collate settings.
There are other possibilities (such as making sure that the file is set to UTF-8 and not UTF-BOM). No doubt you have researched widely, but this question from 2012 resonated in terms of the db content appearing sound, but printing as “????”. I refer you to “PHP MySQL Greek letters showing like ???? marks” where