They could have concentric circles of increasingly deadly threats: start with tripwires, end with landmines. If every time you get closer to the nuclear waste, you're more likely to die, you will probably get the idea.
Remember: the earliest known writings are less than 6,000 years old. We're talking about planning for almost twice that. This is an incredibly long period of time, in human terms (though not in geological terms, which is what created the problem in the first place).
Some of the ideas in the original comment thread from 2006 were nice. Make the area inconspicuous, make it extremely expensive to dig up. Why not make it look like a giant concrete dumping ground?
To thwart geological surveys, maybe you could figure out a way to stealth the tunnels or arrange the tunnels in the shape of a warning message.
Perhaps you should make the area extremely inconspicuous and just trecherous to get to for the technologically unenabled (build rivers, hills etc). That way you ensure that mostly only hikers get there and hopefully don't notice the concealed enterance. Of course, that plan could be thwarted if a group of people seek shelter there because of wartime persecution.