By default, whenever a customized item is added to the cart a new product from that customized item is created in your Shopify catalog if any of the following conditions are met:
a pricing rule is associated with that product in Zakeke.
a thumbnail image of the customized item is created and shown on the check-out page.
Shopify does not allow third-party apps to change the price of a product or to change the check-out page, that's why the creation of a new product is required.
If you don't need those two options, you can easily avoid the creation of a new product by selecting Create a new product only when a price rule is associated with it in your Zakeke back-office > Settings > Shopify settings > Behaviour on the Add to Cart. This means that, as long as your product has no pricing rules associated with it in Zakeke (pricing step when you create the customizable product):
No new product will be added to your catalog when a customer adds the customized product to the cart;
No thumbnail image of the customized item will be shown on the check-out page.
You've got a third option: Never create a new product. If you still want to use the pricing rules inside Zakeke, but don't want the system to create a new product in your catalog, you need to edit your theme code and this is the guide to follow. Please note that you can't apply discounts using the pricing functionality of Zakeke when you set it do to not create new products.