Yes. The Secure Enclave stores the data like a fingerprint, and that data - to the best of my knowledge - is not backed up to the cloud.
https://www.apple.com/business/docs/iOS_Security_Guide.pdf -- pg. 29 under the Health Data subsection.
Edit: @bobwaycott points out the significance of this quote in the below child comment.
Unless I’m misunderstanding you, your quote disagrees with your assertion. Health data is only included in encrypted iTunes backups. It is not included in unencrypted iTunes backups or in iCloud backups.
Of course, that’s just backups. It does say it can be configured to be stored and synced between devices via iCloud, where it is encrypted in transit and at rest. That appears to indicate it is stored pre-encrypted, and does not indicate there is any way to access it outside ones devices.