Hi,
Auctiva is ONLY tracking usage of images that are used on listings submitted from Auctiva's submission service. Submitting listings at eBay bypasses that tracking and would give you false results in the Wizard or other usage info. Unlike Photobucket, they aren't giving a full usage stats mechanism to do deep tracking of use.
If you delete the image, it will stop loading to active listings (after 7 days or flushing the deleted folder).
I don't know if there is a simple method to "poll" all your active listings via the API to build an "in use" list, but that would be a handy tool to help cleanup and "right size".
I don't believe you have any choice but to do the photo by photo check before you delete, at least for now.
Danno