Since the Kendo widgets don't register their scripts and stylesheets automatically, it doesn't really matter where exactly you will put these files, as long as you register them properly. Yes, the Scripts and Content folders (or subfolders of these) are the correct location.
On a side note, if you have the Telerik MVC components in your application, you can use the Telerik ScriptRegistrar and StyleSheetRegistrar to register the Kendo resources:
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