eBay used to close out listings after they sold but have made a change where all listings are now "Good Till Cancelled".
This means they stay up on eBay even when sold out.
The thinking is that you may want to add stock later, but for those that sell mostly one-offs it is an annoyance.
A quick resolve can to select listings in reverse order by quantity (to show all the zero quantity eBay listings) on your eBay Listings tab in JoeLister.
Next, select all of the zero quantity listings and pick Delist in the bulk menu on the top right.