@James Saint-Amour
Welcome to the Community.
In general from my experience, the field configuration page in the admin UI gives you the current stats... However, you may very well having old historical data in your system from your JQL result.
Example - Field A was originally setup for a given project and it was used, however later on the field itself was removed from the project and screen.
I would always trust the field side configuration + looking for JQL results for confirmation (to determine how important are the field values associated to issues in your JQL results, and then determine if the field should be deleted from the system.
In our env, historical data is important, thus we may choose to renamed the field appending "(Old)" before deleting the field. This gives the end users (content owners) times to evaluate if the field information is needed or not. Afterward, we proceed with the action (i.e. delete the field or keep the field).
Hope this helps.
Best, Joseph
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