Just like .css and .log are text files, but I may not want the same default file handler.
What I like is having *.epub open in, say, calibre, but if I append a .zip extension then it will open in xarchive.
Anyways, I open most things from the command line and wrote my version of 'open' so I get what i expect 99% of the time. :)
I'm using KDE3 so I'm not expecting any upstream fixes for this in my lifetime. I can live with crafting my own solutions.
What might work best is if mime types were used by default but forcing behavior for specific extensions was much easier. Get the best of both worlds (which I can mostly do in KDE3 Konqueror but it's tedious.)
Other examples: tar.gz, WAR files, most ODF formats.
Edit: smartphone tyops fixed.
Debian added upstream epub support (and backed out its own) in September, 2011, so this is a pretty recent feature.
If it's bad magic, update your distro. If it's a Konqueror error, file a bug. I'd be surprised if upstream hasn't addressed this (quick DDG/Google doesn't turn up any similar complaints).