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. 

Have you done SKU Migration?
1. If yes - follow this after migration guide
2. If no - follow this before migration guide

Follow the guide below if you have not done SKU migration

At the bottom in the "Variant specific" section you can select which variants you would like unpublished by de-selecting the "Publish" checkbox.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.

Follow this guide if you have done SKU migration

After SKU migration, you will notice that the user interface for Publish has been changed. "Publish" checkbox is no longer in the Variant specifics table. However, if you scroll all the way down, you'll see it here under Product status