If you're not using Classic mode to run any older apps, then you can delete the OS 9 folders without any problems they certainly aren't needed to run any of your OS X apps.
If at a later date you do need Classic (say for example you get your hands on an older app which needs OS 9 to run) then you can reinstall it from your Mac's install disks if memory serves it's on a disk entitled something like 'Additional Software'.