Unsure if this qualify as a bug, but it is a bit annoying!
As the title says, deleting a script while it has assigned a keyboard shortcut results in the shortcut being kept in the user.aseprite-keys file, meaning it shows up when trying to assign shortcuts to other scripts.
The only way to get rid of this is to manually tweak the user.aseprite-keys file with a text editor. So it would probably be cool for Aseprite to check if a script of that name exists, or if the shortcut data needs to be deleted from the user.aseprite-keys file so it no longer shows while editing shortcuts.
Very low priority I would say, and thanks for reading!