All of your points are very interesting, and it has been at the front of my thoughts for a few weeks, as I am writing a novelisation for my new chapter, based around the 34th Millennium.
Firstly, void relay networks and hive cities. I would assume certain primary hive cities on a hive world would have access to some form of shielding from orbital bombardment, and could withstand a certain level of ordnance from surface weaponry. However, how would these shields operate? The central thermal core of a hive city supplies power to the rest of the hive, so a shield network covering the immense size of a hive city ( even a moderate-sized one with a population between 1 and 3 billion) would be a massive drain on resources during a major siege.
Secondly, infiltrators. Say a chaos horde attempts an invasion of a hive city, but cannot rely on hundreds of millions of soldiers or daemons to do it. How would they break through? Could it have been planned for some time? Grow a cult in the underhive, get people of influence within its ranks, and when the time comes sabotage structural weak-points, like cannon emplacements, shield generators, food stores and the like. How would they sabotage them? render them useless, or direct detonation of armouries?
Thirdly, if they did sabotage such key weak points, what would the impact be? I would expect the detonation within an armoury would be cataclysmic, especially near a macrocannon emplacement. The tonnage of explosives meant to defend against capital class ships would core entire neighbourhoods, and bring spires down around them. What disorder would follow? Could major gates be forced open by agents of Chaos from within?
Finally, multiple level- assault. could this be done by jump troops breaching a hole in the defence network? Berserkers forcing a hole through, massed firepower through a small gap in the defences? Again, it depends on the city, its defences and how it responds to such an invasion. Would it be better to strike at the spires first and work your way down, or form en masse at the gates and punch through the walls with high-calibre weapons. Again, the best way to consider it would be similar to the War for Stalingrad in terms of real warfare.
I would read through the Iron Warriors story regarding the siege of the Shardenhold- a city built upside-down in a cave system by a warsmith loyal to the Emperor. The way he defends it is quite something, I would definitely read it.
The writers of the Siege of Terra have been doing excellent work approaching some of these questions, but I guess with all written lore it is best to focus on the micro-level, then expand to the macro size. Work out what the target is, the end result, and then marry the two together according to the major hitters and the sizes of forces present.
Well that's my two cents anyways