As per current functionality, if webhook is enabled for the below events on a Project
Issue link Deletion
WorkLog Deletion
Comment Deletion
Issue Deletion
Project Deletion

and the Project is deleted, then webhook is triggered for
Issue link that gets deleted in the Project
WorkLog Deletion that get deleted in the Project
Comment Deletion that gets deleted in the Project
Project Deletion that gets deleted in the Project

but no Webhook gets triggered for Issues that get deleted in the Project.

A webhook should also be triggered for Issues that get deleted in the Project or there should be some config available to enable/disable webhook for individual events in the Project on Project deletion