Well indeed they are cloneable because when I save cloned fields, the raw Array is printed correctly. However after saving/updating a post or reloading the post edit screen, only one box is visible and the cloned ones are gone. Of course after updating the post there remains only one item in the Array.
In order to check if I did any mistake I changed the field type to "text". All cloned fields were visible with the correct IDs as values.
I am using taxonomy_advanced with custom taxonomy terms on a page template along with the Metabox show/hide plugin.