Yes, Pipemonk does support line items discounts. For the detailed description, see the below explanation.
This is how a product description looks like in your Shopify account. One can easily see the discount associated with a product. (See below image)
This is how Pipemonk syncs products and line-item discounts in QuickBooks Online. (See Below Image)
As you can see, we sync line item discount separately for each product to make your reconciliation super easy.