I think, the files without icons treating as hidden is not a good approach, since every file is hidden by default. For example, on Linux only the config files or app's private folders are hidden. This is a bit different story.
Somebody wrote here earlier, that some tutorials would be good for starters. Maybe, this could be the best solution. This could be a video presentation about the basics of the OS, placed on the install CD. There is a lot of free space on it yet.
The install CD could contain more documentations too. MorphOS library has the lots of useful docs.
