Does restaurant has to pay GST on food being sold through ecommerce operator?

Your sales are not falling under RCM but in E-commerce operator transactions. If it is b2b transaction and you choose RCM then it will show liability on your customer instead of ecommerce operator.

Moreover in restaurants nearly all supplies are b2c. Since you are not liable to pay GST you will show your supplies as nil rated in GSTR-1.

For GSTR-3B I have already told above