Shopify's built-in abandoned checkout email system, unfortunately cannot handle orders created via the Shopify APIs when those orders are created via the Discount Ninja Sales Channel.
To configure the use of the Discount Ninja Sales Channel, please go to Settings > Integration > Sales Channel in the app.
Discount Ninja has notified Shopify about this issue in Q2 of 2020.
Additionally, a public forum post is available that discusses the same: https://community.shopify.com/c/Shopify-APIs-SDKs/Why-can-t-Abandoned-Checkout-emails-be-sent-for-orders-created/m-p/1004228#M60664
If you are using the Discount Ninja Sales Channel we recommend you evaluate other options to handle abandoned checkout emails, such as Klaviyo.