"apt-get update" just keeps your list of available packages synchronised
with the repositories present in your /etc/apt/sources.list file,
it does _not_ download/install anything.

So, when do you see those error messages? When trying to launch
a java program from the CLI? What do "type java" and "java -version"
return? Also, do applets work under mozilla/konqueror?
That would indicate a properly working jre...