Same question here. I was on the phone with google adwords today regarding policy adherence for my site and took the time to ask about this. It appears to be on shopify's end, and sadly there is no way to manually set shipping rates for an item in the google shopping app [that I've been able to see].
My shipping rules are set that any order above $49 is free ship, and anything over $49 on my site gets this "Shipping Rates can't be blank" warning. I'm speculating, but possibly shopify leaves this value blank in the table if you are set to free shipping on that item and since it is not '0.00' google shop is throwing an error? That is at least what it appears like for me.
Im going to attempt to setup a data feed in google merchant center as opposed to continuing to use the google shop app and see if this fixes the problem. If it does, or I find any other fix I will report back,