By default, Shypyard rate limits Shopify API calls based on the number of workers for your Shypyard plan and the refill/bucket limit for your Shopify API which is based on your Shopify plan.
If you want to increase throughput, then you can add additional Shopify integration in Shypyard, and alternate the API calls to spread out the rate limits.
For example, lets say you added 3 Shopify integration in Shypyard. Then you can use those 3 integrations for different tasks
const shopify1 = libs.shopify.get('shopify1');
const shopify2 = libs.shopify.get('shopify2');
const shopify3 = libs.shopify.get('shopify3');
// 3 separate credentials so subject to separate rate limiting!
const products = await shopify1.product.list();
const customers = await shopify2.customer.list();
const orders = await shopify3.order.list();