its as simple as killing the planet
Well, this is the issue. It's not that simple to kill a well defended planet. (Of course against the AI it's simple, but actually anything against the AI is simple.
There are planetary shield generators which could spoil your bombing. (Shield generators are easily defended with gauss cannons.)
And if your enemy doesn't has a fleet there capable of killing your siege frigates, well, his fault for just relying on his gauss cannons imho.
Of course this needs balancing against bombardment damage/speed of frigates and capitals, but it would act a good tactical option.
But you're right in one point. We need the ability to place structures in 3d for this. Some gauss cannons on the north and south pole of a planet are needed against small fleets which try to exploit the positioning of your gauss cannons.
Against heavily defended enemy planets you could try to kill their defenses first and then kill the planet without interference, or you could try to kill the planet first and then prevent the enemy from recolonizing while his defenses are still online.
What do you mean by that? My bombers would make short work of something anywhere in the system.
Well, my flak frigates would make short work of your bombers.