Noticed this post has been up here a while with no responses. Did you ever get a solution to this issue as I am having exactly the same one. Google has suddenly stopped listing my products, pages etc correctly in search results. Everything was fine until a few months ago and visitor numbers (and therefore sales) has fallen through the floor since. Somebody, either at Shopify or at Google has altered something and is now having a very severe impact on my business. Of over 1500 pages listed in my sitemap, nearly 1300 are blocked by the robots.txt, a robots.txt that Shopify seem unwilling to allow those of us paying for their service the right to access and amend.
If anyone has any ideas or suggestions to get this situation fixed I'd be pleased to hear them, if not I'm going to have little choice but to move to another ecommerce service where I can actually start selling again.