>The Onkalo repository is expected to be large enough to accept canisters of spent fuel for around one hundred years, i.e. until around 2120.[10] At this point, the final encapsulation and burial will take place, and the access tunnel will be backfilled and sealed.
So they're already planning to fill the tunnels completely. Considering the depth of the main facility, I would think this will make it very difficult for a primitive civilization to reach the facility even if they found the former entrance and wanted to investigate.
[1] https://en.wikipedia.org/wiki/Permian_Basin_(North_America)
Any significant structure would introduce a gravitational and/or magnetic anomaly. Given that, keeping the structures as small as possible seems the way to go, but of course, you also want to contain the waste for thousands of years.
On the other hand, one could hope that anybody who can detect such anomalies knows about radiation, too.