Hello, Camilo!
The plugin uses the native function provided by WordPress for removing media files. It doesn’t alter it in any way. If your WEBP files are not tracked by WordPress or by the plugin you use to generate them, you get orphan files on your server. (it doesn’t matter if you remove your images manually or automatically with a plugin like Autoremove Attachments)
I’m guessing the plugin you use to generate your WEBP files does a poor job of tracking them.
Also, keep in mind that not all child attachments are removed when the parent post, page, or custom post type is deleted. If an image is used in multiple locations, it will be skipped.
For example, if you have an image attached as a child to a product and you use that image somewhere else (like in the body of a post, a gallery, or if it’s set as a featured image), when you delete your parent product, the image will be kept and attached as a child to the post it was reused in. (it changes parents)
You also need to make sure:
– that your images are actually attached as child attachment to your posts, pages, and custom post types
– that you remove your post, pages, and custom post type from Trash (a soft delete doesn’t trigger the removal of your attachments)