Missiles, damage pulse and I think warheads (their damage is low so perhaps you just don't see it) don't deal HP damage to the planet core.warheads and beams don't deal HP damage to the planet core.
Missiles and warheads explode at the surface, Tried a few combo weapons and they didn't either damage it either so I assume the entire explosion system doesn't work on planet cores. At least it doesn't crash the game/server ^^but only damage nearby blocks and not reduce the HP of the core itself.
Beams go through the planet core and hit the planet plate at the opposite side.