So, this is a charming thought experiment to play with, but are there realistic scenarios where there is a hypothetical future society has the capability of even reaching the depths of something like the Onkalo storage without also having the technical prowess to understand radiation?
You're assuming nature hasn't found a way to expose such sites, despite all our best attempts at finding geologically stable locations.
Obviously we're talking about a low probability event, but the cost of providing such warnings is virtually zero, so why not do it?
(One reason - they might have the opposite effect to that intended. Curiosity killed the ray cat and all).
Isn't this what gothic art was for?
Gargoyles and imagery from Berserk manga would probably do the job. And a mound of skulls, real or not.