Double Whatsapp Backup in iCloud
Yes, if you have device backup and WhatsApp chat backup turned on, you will indeed be making two backups for WhatsApp. In my case, this means 2 x 1.5GB.

The following unofficial info should help you make a decision on whether to keep both, or turn one of them off. Disclosure, this is not my info, I did find it elsewhere:


  The iCloud backup and having the device backup does duplicate data.
  Backing up the phone will back up whatsapp, so if you restored to a
  new phone even without enabling the inbuilt backup your data would be
  there.
  
  If you enable the whatsapp iCloud backup you are able to restore your
  data to a new phone, without performing a full iCloud restore.
  Personally I would keep the in built whatsapp backup enabled and
  untick it from the complete iPhone backup. I swap my backup often
  between my two phones using just the built in whatsapp feature,
  without restoring etc.


Source: https://www.reddit.com/r/ios/comments/3pz8hh/how_does_the_whatsapp_app_backup_work/