Most webscripts store config data in plain text, under normal conditions users cant view/use them.
If a hacker has access to the files of your script it doesnt matter if the data is encrypted or not, he can get it by decrypting them (unless its one-way-encryption).
As for the DB, you have to check it manually if its ok (or send it to an expert here), the "repair" functions that the DB or Hostings offer are to fix damaged tables or db's, not to removed unwanted elements.
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