You will have to go with the assumption that if no issues have been updated in a project for a long period of time (you can decide the period), then the project is no longer being used.
You can use JQL to find issues that have been not been updated for a long period of time.
For example, if you want to search for issues that were last updated before 12th December 2010, you can use the query
updated < "2010/12/12"
Documentation is available here
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