Google really couldn't care less about the code your site uses. As long as the site works, the content is understandable and it doesn't take too long to load, they just aren't interested. Whether it's home-made or an off-the-shelf product is irrelevant.
Have a look at the source code for a Shopify page – does it look OK to you? If so, the question comes down to ... can you develop a site that gives you better value for money than Shopify? If yes, do it. If no, why bother?