I am not greatly knowledgeable with javascript, having said that I would appreciate some answers to my question which is ' If a site has javascript in the header and footer of the page, would it be possible to convert the same into HTML for optimization purpose, so the search engine can crawl to all the pages, if yes how can one go about doing it or ask the developer to do the same"? Hope i have framed the question correctly.....
Nope as Javascript is intended, it only can be used at the viewers side. If you like to convert to html use scripting languages (like php, asp, perl, cgi) that will create direct html into the pages.