Many Shopify themes already support "Microdata" markup that provides the same sort of information that the JSON-LD for SEO application does - things like product information, prices, et cetera. You can check to see what sort of information your theme is currently providing to search engines like Google by entering one of your product URLs in Google's Structured Data Testing tool here: https://developers.google.com/structured-data/testing-tool/ .
The advantage of JSON-LD for SEO is that we not only provide the same sort of information, but additional info about your store that allows Google to include your store on its Knowledge Graph. That allows for functionality like providing a site-specific search box in Google results or displaying a company card in search results.
Providing info via JSON-LD also means that the information about your products is decoupled from the theme you choose. This means you have less to worry about with changes to your theme, and also that as new JSON-LD features come out, we can automatically upgrade your store's markup.
Ultimately, if your store already has Microdata markup (like yours), you may not see any huge benefits from the app right now. On the other hand, having both JSON-LD and regular markup on your store doesn't cause any problems and does mean that Google may choose to offer those extra features like site search and information boxes to potential customers.