You can do better than nukes!
The thing about a real nuke is that the fallout is only dangerous for a while. Things turned radioactive by a nuclear explosion turn unradioactive after a short time. Those tunnels would be full of dusty debris.
Nukes. Flash boom. Ho hum. You have a sweet tunnel world! Soft sci fi it up! Make their bomb something interesting! I am picturing a weird energy release that was hungry for life and that changed and fed on things in its path. Purple tendrils and maybe you can hear them in your mind. Something more than they realized Things came up from the utter deep to join them.
You need to block off those tunnels with serious seals and not for theoretical reasons. Very bad things are in there.