James Rollins has two present-day novels that might fit the bill. The first is Subterranean, featuring an expedition into a vast tunnel/cavern system under Antarctica, where strange creatures have evolved over the vast span of years. The other - which I thought was by far the better of the two - is Ice Hunt, which takes place up at the other pole, where an abandoned Soviet underground ice station is rediscovered and a team is sent to investigate it. There's an enormous cavern system buried in the glacier with the station, and a strange species inhabiting it with an interesting biological capability that ties in with the original Soviet research that went on in the facility.
Since both are set in the modern day and deal specifically with "frozen megadungeons" I'm not sure if they're quite what you're looking for, but I'll throw them out there just in case you might be interested.
Johnathan