When creating an empty MVC 2 project, I have a lot of javascript files in my Scripts folder. Why? Will removing them affect my application?
No removing them won't affect anything, unless they are being used in pages. However you said this is an empty MVC project so you'll be fine.
They're there for you to use, to make your life easier. For example, JQuery is included.
Take for example JQuery file, It provieds functions which has solutions for crossbrowser related issues which makes developement easy. Similarly other files has functions whcih are providing readymade functionalities which can be used for rapid developement.
Unfortunatly as JS is traveling to browsers its downloaded on the client. Its suprising for not JS people as its not like .NET api where one or more dll is sufficient for all the api and developer dont have to worry(some times :)) about from where they are coming.
I will suggest you to study included JS files and include/use only those which you really wanted to use.