Hi @streetlifebahrain,
The pages you mentioned where the breadcrumb is coming, those pages are WooCommerce default page, and the breadcrumb is rendered through the header. In the Cart and the Checkout page, the specific page template has been selected which does not have the header with it and that is why the breadcrumb is not appearing on these pages.
I would suggest you set the default template for these pages and try by removing the navigation section as you have done in WooCommerce pages, or else as suggested by my colleague you need to upgrade to Pro where you can have the option to customize the headers.
Thanks