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
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.