I think its safe to use ResEdit to make Mac OS X files and folders visable in os9. I wouldn't mess with the kernel, though.
Use the getinfo option in res edit.
PS: if you are wondering how those files became invisable in the first place, check on the 10.1 installer cd (probably on the 10.0 installer cd, too) in /Library/Installer/Packages/Essentials.pkg/Contents/Resources/
There a list of files to make invisable, and a program called MakeInvisable, I think. I'll post some corrections later as soon as I get to mess with my G4 and the 10.1 cd.