You need not to be worry about java scripts. If you want to use its and do want to cached by google, It is possible. Google bots does not cache javascripts . I am sure because I use in my sites and when check caching never seen.
Yes, it can. If your JavaScript files contain critical information, such as your menu, then the search engines will not be able to crawl and index them. However, if you use the scripts to enhance your content (like how the Son of Suckerfish CSS dropdown menu provides Internet Explorer 6 with a class on list items that can be used to make the nested dropdown list sappear) then you'll be fine since the content will already be in the HTML source code.