WhatsApp is backed up in iCloud Storage and iCloud Backup
Deleting one does not affect the other as they are backups of different types.


The backup in iCloud Backup (first screenshot) is a backup of the contents of the app container on your iPhone. This is backed up every night as your iCloud Backup takes place, or manually when you Back Up Now.
The ‘backup’ in iCloud Storage (second screenshot) is a backup created by WhatsApp using WhatsApp Settings → Chats → Chat Backup. This is backed up at most per the interval set in WhatsApp settings, or manually when you Back Up Now.


It is up to you which backup you choose to keep. Personally I would use WhatsApp own backup service with iCloud rather than iCloud Backup.