Cleanup

No. An image that only comes from another plugin's table at runtime, or sits in a theme file with a hard-coded path, is not found. That is why the image is shown next to every row. And that is why the plugin deletes nothing on its own.

Media moves images with an entry to the trash: they disappear from the media library, the file and the entry are kept, and WordPress never empties this trash on its own. Because WordPress hides it by default, the “Clean up” area has the button “Open the media library trash”. There you bring an image back with “Restore” or delete it permanently. Only files with no entry at all are deleted straight from the disk. There is no trash for those, and a confirmation comes first.

Because they may be in use. The page usually shows the smaller sizes WordPress has generated anyway — the large original mostly just takes up space on the disk. For new uploads, the “Big-image threshold” in Kakapo Performance, in its “Images” area, sets the edge length from which WordPress scales them down. Neither plugin shrinks originals that have already been uploaded.