Regarding that moon, or more exactly the asteroid Regula, my hobby-horse here is that it was the Genesis planet.
After all, it appeared to be the only solid object of appreciable size in the system, and Genesis was detonated within that system (within just a few impulse-minutes of Regula, that is). And Genesis was designed to transform a dead moon into a living planet - and probably wasn't capable of facing a markedly different challenge, considering how only the technologically backward Khan could have reprogrammed it, and how even the very makers of the device had claimed that they could not "cram a single byte" to the already high-strung system...
Thus, the cave would be gone at the end of ST3 where the planet supposedly breaks up. A neat package as such.
As for whether Genesis would be a good superweapon, it's still a torpedo. Starfleet supposedly has defenses against somebody torpedoing its precious planets; if it didn't, "conventional" antimatter warheads would already have erased life from Earth and carried the Klingons to victory. So what if Genesis can do with one shot what antimatter technology might need five torps for - one can always ripple-fire, and it's easier to saturate defenses with well-understood and probably cheap antimatter torps than with complicated and no doubt expensive Genesis warheads.
Timo Saloniemi