This could take a while, and I'm not even sure if it would work, but it should.
OSX identifies an invisible file by the "dot" preceeding the file name ( eg .ds store) while OS9 uses a "flag" to make files invisible. So, in theory this should work (try carefully first).
Get a copy of ResEdit and install it in OS9. Select your OSX files and set the flag to "invisible".
Warning: ResEdit is not for the faint of heart. Heed the usual warnings (always use a copy of original files, save and test, back up everything, etc.).
I might try by first placing a file in an obvious place (say at the root level of your HD) and while in OS9 naming it to something like " .testfile ". Set the flag to invisible in ResEdit, and confirm it is invisible in OS9. Check that it doesn't show in OSX (it shouldn't). Then try with one OSX file that again is easy to find, and make sure OSX can still find it if it needs to by booting and running OSX for a while.
I wouldn't bother with files that you normally won't see in OS9 (say, the entire OSX system file or library folders in your user folder).
For more info on ResEdit, go here: ResExcellence Site In fact, poke around here a lot to see if anyone has tried this before and to get an idea of what kind of trouble you could get into if you don't play safe. Or, even better, ask if this is a good idea in the User Forum as I'm sure it's occoured to someone else.