Shopify Plus customers can create a number of different types of scripts using the Script Editor. Some of these scripts (typically shipping scripts and payment scripts) are complementary to what Discount Ninja offers. Other scripts (line item scripts that implement discounts) can be replaced by Discount Ninja.
By default Discount Ninja creates discounted checkouts using Draft Orders. In this mode, Shopify will not execute scripts. The documentation explains:
Line item scripts, shipping scripts, and payment scripts don't work with draft orders or the draft orders checkout.
However, Discount Ninja also supports creating discounted checkouts using the Checkout API. In this mode, Shopify scripts are executed on the checkout.
To ensure you're using the Checkout API, you'll need to install our free companion app (Discount Ninja Sales Channel) and configure the app to use the sales channel.
Note that using the Checkout API implies a discount field will be available at checkout. You can read more about that here: https://support.discountninja.io/en/articles/3497171-checkout-discount-field