Update will patch security holes outdated versions have opened
Malware can be removed from hosting account, Updating your scripts will patch the security holes the outdated versions have opened.
Vulnerable Applications: Any of web application might infected from virus or malware.
No, renaming the file will not keep your site safe from it being exploited again. As I noted in my previous response, if you wish to prevent your site from being hacked again through the exploit of the bookmarks script, you will need to disable, remove or secure the bookmarks.php file to prevent further exploits.