Hello, Egg!
The cook tool does its job with the project that you give it. If (for example) you use the Cook Tool to work on the exported version of it, it will create a build based on that. There isn't any file duplication unless there was a mixup in the setup.
In addition, if you use newer versions of NW.js in your project (configurable in the project settings) it can add about 400MB to the final build. It's normal that newer versions of it can make the final build bigger. Finally, the included asset compressor (found under the utilities menu) can help in compressing the game's files by using more modern image and audio formats (which are more efficient in compression.