How can I safely restore data from iCloud if my iPhone has been compromised?

By hack, if you mean a stranger is remotely controlling or monitoring your device, then...

Keep the iPhone updated to the latest iOS always and never Jailbreak. That's it.

iOS / iPadOS devices cannot be hacked or infected with Virus / Malware / Spyware if it is updated to the latest iOS/iPadOS unless you have intentionally downloaded spurious software or unauthorized apps directly from the internet and installed them on your device or/and have Jailbroken. 

It (Hacking) also depends on how careful are you in sharing sensitive and valuable information pertaining to your iPhone such as Passcode, Password, etc with your friends and family members.

Be careful when sharing the device's sensitive and valuable information with friends and family members.

Thumb Rules:

1. Enable  Guided Access before handing over an iPhone to kids or to a stranger.
2. Don't share Apple IDs
3. Don't Jailbreak
4. Don't share sensitive information pertaining to your device and payment methods
5. Beware of Phishing
6. Do not share your location with a stranger --> Find friends and share your location with Find My
7. Don't plug in your device in Airports and Public places through third-party cables and trust the device. Beware of Juice Jacking. (Especially in India)
8. Do not leave your iPhone unlocked and unattended in public places like offices, schools, malls etc.
9. If you see this --> What to do if you get an alert that an AirTag, Find My network accessory or set of AirPods is with you

To avoid your WhatsApp account being hacked, please take the following steps

1. Enable FaceID for your WhatsApp Account
2. Enable Two-Step Verification for your WhatsApp Account
3. Do a periodic check of your WhatsApp Settings to know if someone has unauthorised access to your WhatsApp Account

If someone gets hold of your device even for less than a minute they can have your WhatsApp hacked. Do a periodic check of your WhatsApp Settings to know if someone has unauthorised access to your WhatsApp Account. If found, do log them out

Please see the pic below

This feature is provided for you to have access to the same account across all your devices. At the same time, if you are naive, you are hacked!

WhatsApps' Link a Device feature can be used by anyone if you...

1. Have not enabled Guided Access before handing over an iPhone to kids or to a stranger.
2. Have shared your Apple IDs
3. Have shared sensitive information pertaining to your device
4. Have left your iPhone unlocked and unattended in public places like offices, schools, malls etc.

About linked devices | WhatsApp Help Center

WhatsApp is not an Apple product. Contact the app developer here --> App Support or WhatsApp FAQ  Or Restoring your chat history - WhatsApp FAQ or Contact WhatsApp

WhatsApp Business is not an Apple product. Contact the app developer here --> Developer Website  or App Support  or WhatsApp business products - WhatsApp FAQ

Instagram is not an Apple Product. Contact the app developer here --> App Support  or Instagram Help Center or Troubleshooting

To be clear, they are not getting your information from your device. You do not have malware or a key logger on your iPhone as nothing can be installed in the System Folders even if you wanted to.

What you described does indicate accounts have been compromised and I would recommend to contact Meta as they own both of those apps. I am sure you are well aware of the many scams on those platforms where users have found their account compromised. Also note that another user you are communicating with may have had their account compromised where all of your communication with that person would be visible to them.

Review the information you have allowed WhatsApp and Instagram to access on your device. If you have granted them access to your Contacts and Photos, you may want to reconsider that. Also note in the Privacy Page for Instagram in the App Store the information Instagram collects that is linked to you:

• Health & Fitness
• Location
• User Content
• Purchases
• Contact Info
• Search History
• Financial Info
• Contacts
• Browsing History