There are several ways to delete mail in the Mail app of macOS Mojave. To delete a message from a Mail notification or with a swipe, the “Move discarded messages” option in Viewing preferences in Mail must be set to Trash; otherwise, the message is archived.
In a Mail notification: Move the pointer over the notification, then click Trash.
In the Message viewer: Do one of the following:
Swipe left with two fingers, then click Trash, or swipe all the way to the left until the message disappears.
Move the pointer over the message header, then click the Delete button (it looks like a trashcan) that appears.
Select a message in the list, then click the Delete button in the Mail toolbar.
(This how-to is based on my experiences and info on Apple's support pages — where the images sometimes come from.)