How to hide src folder from Eclipse Project Explorer?

This is actually not added twice it is because of the explorer view you are using, just change it to navigator view and your problem will get solved.

Check this post might help you more, it is not related to you answer but show how to select navigator view Hope this will help you :).

Click to the third right top button, then "Filters" and then check "Name filter patterns" and write "src". Then the second src folder is hidden.