Why does Recapture show more carts than Shopify?

Recapture will always show more carts than Shopify because Shopify only stores checkouts (where a customer attempted or completed checkout at the Checkout page of your store) and not just "carts" (which is something in process, before they ever reach checkout) .  Unless the customer starts the checkout process and enters their name/email on the checkout page, Shopify will not store the details.

Recapture, on the other hand, stores carts in ALL states--whether they have reached the checkout page or not.  Even if the customer never starts the checkout process, the cart will always appear in Recapture.  Recapture also has better ways of capturing the email address and associating that to the cart--via email popups (email collectors), our Add to Cart Popup, or being able to listen for other email-collecting widgets already installed on your site.  

Recapture is simply better at tracking your customer's behavior on the site than Shopify.

This is one of the advantages you get with Recapture--better visibility into your store!