Sending a notification that someone has replied to a comment does not send e-mail addresses. My plugin will only send a notification to the original comment author when a comment got a reply, which uses a template like this:
Hi <name 1>,
<name 2> has has replied to your comment on
<link to article>
<comment text>
Click here to reply (link to comment reply function)
Click here to stop receiving these messages (link to unsubscribe from this)
But this does not contain not contain any e-mail addresses. Maybe you confused sending e-mails for comment replies and sending e-emails for comments which is done by WordPress itself when you configured that accordingly. WordPress will send an e-mail to site admins whenever a comment was written.
When a plugin is disabled by WordPress, it will not be used any longer. Deleting a plugin is done in WordPress by selecting “delete” in the plugin management. This will delete all files of the plugin.