Most of the required typings are not there, plus you have an extra library with minified files.
Please remove (not disable, but delete) all d3 libraries in Settings | Languages & Frameworks | JavaScript | Libraries, re-start the IDE and then try re-downloading the typings through Alt+Enter
Works fine for me with d3 typings installed in Libraries:
can you repeat the issue in a new project?
Are you using IntelliJ 2021 ?
Anyway new project same issue.
Steps:
npx create-react-app test
cd test
npm install d3
Can't reproduce with your steps
Please expand the External Libraries/Global @types/* node in the Project tree - what can you see there?
In addition, if I hit Alt+Return I can't see the Install Typescript definitions menu

Most of the required typings are not there, plus you have an extra library with minified files.
Please remove (not disable, but delete) all d3 libraries in Settings | Languages & Frameworks | JavaScript | Libraries, re-start the IDE and then try re-downloading the typings through Alt+Enter
Thanks your suggestions solved my problem