Right, that folder is used for client side scripts. For example, if you have a validator at your page, and have the client_validate property set to true (or something), then the ASP.NET page uses WebUIValidation.js.
These files are needed if you use these kind of actions, elsewhise, just leave them, just in case (because I don't know if the framework creates the folder itself).
Ow, don't try to replace them. This will call an anoying error during the load of the page, and ofcourse, the function won't work.