It would be trivial to find a directory. You would be left with a bunch of boxes with things in random places, and programs possibly looking for non existent dirs.
But for simple devices or server setups with few changes over time, it might be worth it as it would at least cause a little more work to hack in. I remember that it used to be encouraged to use non-standard paths for security's sake, but then it seemed like too much work for the reason you stated. But these days, with more automated attacks relying on standard paths, I don't think it is out of the question.