Windows does the same thing, except that they're usually hidden directories/files (i.e .ini), MacOS/OS X does the same thing (i.e. .trash). If you just can't tolerate them, delete them but don't be surprised if an active app pops up some kind of error message. If this does happen, quit the app and start it back up, but keep in mind the contents of that 'Android' folder will just get rebuilt/restored. There's an equivalent residing in your device's internal storage (that should be left as is).
Think of it this way, the operating system and apps should be left to do what they need to do, once you start micromanaging things like basic system folder/file management, all you're doing is gaining a false sense of accomplishment that in reality is only making your device do things it doesn't need to be doing.