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See this page. The short answer is that the GPS coordinates get turned into a UTM pose, and that UTM pose needs to have a yaw so that we can generate a transform from the utm frame to your world frame (e.g., map). Forgetting GPS positions for a moment, the UTM grid is a world-fixed coordinate frame, just like map or odom in the EKF. If you want to transform coordinates from one frame into another, the orientations of those frames are required. You need to know, at the point your robot started, which way it was oriented in the utm frame, and where it was in the utm grid positionally. Those two things define the utm->map transform (or utm->your_world_frame, whatever that is).
That's only true if you turn use_odometry_yaw on for navsat_transform_node. The EKF itself doesn't care about earth-referenced headings. If that's in the documentation somewhere, can you point me to it? Sorry for the confusion.
navsat_transform_node will publish GPS messages at the rate at which you tell the node to run. It's running on a fixed update timer that runs at the rate you specify. The poses that it _outputs_ are driven by the latest EKF output. So it takes in the fused output from the EKF, transforms it back into GPS coordinates, and publishes.