In order to unpublish an item on Rakuten you simply have to go to your Shopify product page, click on "More actions" then "Rakuten - Edit Product"

A modal will appear allowing you to edit your Rakuten item information.  At the bottom in the "Variant specific" section you can select which variants you would like unpublished by de-selecting the "Publish" checkbox.

Note: You can also unpublish a product by making the Shopify product unavailable to the Rakuten sales channel.