1) if you installed it ontop of an old install java may have been unchecked in that install
2) yes it is unchecked by default on a new install, I believe this was changed (or done) because of the fact that many people had software (mostly games) which were being destroyed in the java cleanup
so it cleans all files in the java Caches referenced above. Often those include settings for programs (In my case it includes the Settings for the Daytrotter music downloader program) I still do check my Java cleaning in CCleaner but added an exclude so it kept my settings for the software. However this took a while to work out what folder to exclude, which is something many users weren't willing to continually lose their settings to test and find.