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For an overview of the abuse feature you might find the following helpful - Setting Up Abuse Reporting
However, in regards to your specific questions:
Where does the content go when a content is "Rejected"?
Nowhere, though it is hidden from the view of users.
Does the user who's content is Rejected still see the content?
Yes, they will see a message similar to:
Does the user who's content is Rejected get a notification and/or Moderator Notes?
Yes, they will receive a moderation notification:
Can the moderators run a report for the "Resolved" Moderation Queue?
This type of report is not currently available in the OOTB Jive platform.