My guess is it is a folder in the virtual file system, meaning the files are ultimately stored in a content DB. "Scripts" in this case is not a document library, but a folder. But, since the folder doesn't really exist, you can't see its contents by just appending /Scripts to the app URL.
If you want the content you are deploying to be accessible in that way, through a browser, you will also need to deploy a document library where you want that content to go. Here is a sample module Elements.xml that deploys a couple JS files to a document library called "Scripts". Keep in mind that the document library is also part of the same app project.
<?xml version="1.0" encoding="utf-8"?>
<Module Name="ScriptDeployment" Url="Lists/Scripts">
<File Path="ScriptDeployment\jquery-1.8.2.min.js" Url="jquery-1.8.2.min.js" ReplaceContent="TRUE" />
<File Path="ScriptDeployment\jquery.SPServices-2014.01.min.js" Url="jquery.SPServices-2014.01.min.js" ReplaceContent="TRUE" />
Using this method, if I browse to https://my/app/url/Lists/Scripts, then a normal document library list view comes up.