You’re right - that’s why push notifications data usage is shown under system usage, not per-app usage. When an app wants to send you a push notification, it notifies Apple via the Apple Push Notification service (APNs) – original name, I know – who then relay it onto you.
Apple Push Notification service (APNs) propagates push notifications to devices having applications registered to receive those notifications. Each device establishes an accredited and encrypted IP connection with the service and receives notifications over this persistent connection. Providers connect with APNs through a persistent and secure channel while monitoring incoming data intended for their client applications. When new data for an application arrives, the provider prepares and sends a notification through the channel to APNs, which pushes the notification to the target device.
from here, if you’re interested.