Well, as far as I know, OS9 file comments are in the Desktop DB (vs. .DS_Store under OSX). If you have modified the copy script to copy that, and it's unmodified (as I'm sure it would be), I don't know why the comments wouldn't be visible under OS9, since the involved files (once you changed the copy script) would be copied... especially if you've named the volumes the same. We certainly copy all the resource fork info, the files, the other metadata elements, etc.
Regarding why the Desktop DB isn't copied, as I recall (again, this is some time ago, and in a search of our internal database I can't find the exact info), the system wouldn't always start up properly under OS9 when the Desktop DB wasn't rebuilt, and not copying it was the recommended 'fix' (as opposed to forcing users to do it manually).
We haven't changed the way this stuff is copied for some time, so I don't think an earlier version of SuperDuper! will help, although you're welcome to try with v2.1.4, which you can download from the sidebar on the SuperDuper! page. But—and I hate to be discouraging here—given the fact that OS9 isn't available any more, and there are no current Macs that can even run it... and that we were always an OSX program and not a MacOS program, I can't say we've ever focused on OS9 support except as an extension of ensuring we're copying files properly.
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--Dave Nanian
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