Yoast has an ecommerce plugin so use that.
It has a bit more functions specifically for ecommerce sites.
To answer the 2 questions:
Should i noindex the media and also the custom post type archives for product and gift cards and if so why?
- noindex is fine
What about the taxonomies for ecommerce? What's best practise? Noindex?
- noindex is also fine
On the sites I've worked with using that setup, those worked out fine.
