Apple Pay only tokenizes card information once when the card is added to the Apple Wallet on a device, not for every transaction. This means that usage for an on-device tokenized card can still be tracked until the card is removed and re-added.
More recently, an additional identifier uniquely identifying the underlying card has also been added [1]. That one persists even across multiple devices and token deletions.
[1] https://www.level2kernel.com/payment_account_reference.html
If it's actually encrypting information (not just signing it), then that's another thing entirely, but signatures don't hide data.
But that's not necessarily the case either, as somebody else brought up the fact that identifiers ARE in fact passed to the merchant.