That kind of creative copy-protection is infamous, but for largely institutional or personal records, most people wouldn't have gone to that level of trouble just to obfuscate data. If they had, then we may miss out on some hidden data, but I don't think that argument alone can justify keeping around any type of storage medium that may have a timing trick, hidden filesystem, or other form of protection. At the same time, folks have developed functional technology to record timing information as well as bitstreams and sector information when creating a disk image, so if there were the type of tricks you describe they could be reverse-engineered later.

You make a good point about no medium being truly obsolete. As long as there's enough funding, that is. Also, archivists get rid of things all the time through deaccessioning or weeding, and with physical storage space always being at a premium, it prompted my question.