Maybe you put it wrong. Nuke clears stuffs. Instead of mining the blocks or stuffs in ur realm, that is when we use nuke. It do the work in just a sec :).
Nukes only blow up blocks at the same level as it and above. So nothing below the nuke will be destroyed. If you want to clear a realm. dig to the bottom of the realm and place the nuke there. It will then destroy every block in the realm.
You probably placed it wrong. It's meant to blow up all blocks at its level and above. If you placed it at the top, it didn't blow up anything because you're supposed to put it at the bottom if you want all blocks cleared.
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So nothing below the nuke will be destroyed.
If you want to clear a realm. dig to the bottom of the realm and place the nuke there.
It will then destroy every block in the realm.
xD*