We are sorry to see that you are having problems with MultiPHP option. As far as I can say, the # will not add automatically on .htaccess. We would suggest to submit a ticket to the help desk, so we can check this.
If you deleted the mail from your mail client when using imap protocol, the email should be deleted from the server too. There is no question on that. However, if you deleted those mail within one week, we can try to restore the mail folders from the backup server. To check the availability of the backup, please submit a ticket to the helpdesk.
Many clients are using Wordfence WordPress security plugin and we recommend you to use the same. We didn't see any load issues only with the Wordfence plugin. Most of the clients are having positive reviews with Wordfence.