The messages won’t be interfered with as that is stored by phone number. Backups will clash though as 2 different backups will be created of separate chats. One could be deleted at any time and the other device could be backed up.
If you want backup enabled I recommend using another Apple ID as it is backed up using iCloud.
From this WhatsApp article:
To make a manual backup of your chats at any time, go to WhatsApp > Settings > Chats > Chat Backup > Back Up Now. You can also enable automatic, scheduled backups by tapping Auto Backup and then choosing your backup frequency. This will back up your chats and media to your iCloud account and you can choose to include or exclude videos from the backup. The iCloud backup process can take a while to complete, depending on your Internet connection and backup size.
The WhatsApp messages will be different but FaceTime conversations will be linked as it is Apple ID linked. Bear in mind without backup chat history can be lost.
You won’t be able to FaceTime to the same Apple ID devices but you can call each other on WhatsApp.
In FaceTime settings though you can select what you can be reached by and use different emails:
Go to Settings -> FaceTime and choose how you can be reached: