Although there is a “Delete” option in the Admin, there is no way to actually delete products and SKUs. The correct approach is to deactivate them.
To deactivate products or SKUs, simply uncheck the “Activate if possible” option within the SKU, as described in this documentation:
If you don’t want to see inactive products in your store, you can filter by active products only. See the screenshots below:
What happens is that, once the product in question has any reference to another area of the system (which is quite common), it is no longer possible to delete it from the database! 
This information is described in the documentation: How to delete a product from the store | VTEX Help Center
That’s why we recommend deactivating products instead.
If deactivation is not an option, you can reuse the ID of those SKUs and products by changing their names. This way, you can use the same ID for a different product.
For more information on how to deactivate products in bulk:
Dúvidas Frequentes: Como excluir itens do catálogo em massa? | Como excluir SKUs em massa? | Como excluir Produtos/SKUs do catálogo?