They should show up under System Settings → Data Management somewhere, probably under the same name as they showed up in the eShop. That should allow you to uninstall the whole lot in one go. Unsure if it will take down anything else with it, tho.
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You can choose themes in your installed titles in freeshop and delete them from there. You will still have the tickets for all of those themes and will be able to re-download the ones you want from the theme store (for free) afterwards.
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