I don't believe you can prevent an app from accessing the data it needs to work.
The only way to stop it would be to remove that app.
The app should be GDPR compliant and include a privacy policy:
https://shopify.dev/tutorials/add-gdpr-webhooks-to-your-app
If you have specific questions about an apps GDPR compliancy, you should reach out to that developer with your questions.
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