i have faced on gmail, and than disable sync All Mails and problem solved for me.
open gmail, go settings>your email adress>Manage labels> Inbox(ALL) and All mail not sycn
My settings are here.
I don't know whatsapp issue :/
Same issue happened to me. I just found that it is related to "lock screen" theme i used. I changed lock screen theme, and duplication problem solved. I checked and found that several themes cause duplicate/multiple notification.