The format that you are using is outdated.
The previous format does not support new innovations like below
Ability to use Source Tracking
No more need to maintain package.xml in Source folder
Create 2GP packages from the Source folder
Ability to break Custom Object metadata into manageable format
You can read more here.
Hence I suggest you move to source ...
The file is described here. It is used to provide JS language support in VS Code. Technically, you could delete all the duplicates and place a single copy at the project root, as you suggest. However, this may cause improper language support for Aura, Visualforce, and third party scripts in Static Resources. Try it out and see if it works for your project. ...