The thing to remember about the Arcology under Deus' control was that it wasn't just static defenses you had to worry about, but mobile and VERY adaptable ones. In the Renraku Arcology:Shutdown book, it says that very quickly Deus had taken over the majority of the Red Samurai garrison(which I can't remember how many they had, but it was a fair bit, I'm guessing in the mid to high double digits). And each 5-man Red Sam team has an awakened member among them by default(usually magicians but sometimes adepts or mystic adepts). They had placed quite a few high-force wards and barriers around the upper floors, as well as other key floors and locations around the Arcology(again right from the book), so the important bits were magically protected as well.
Now, they can hardly ward/barrier the entire arcology obviously, but this is where the mobility and adaptability oif Deus' defenses came into play. If he didn't like the way something was shaped, or exposed, he could have spider drones and the Greens reshape the entire area, and then reinforce the walls using Leech constructs, which also detected magic and let out an ear-piercing wail when they did. Or, if he felt something made just a little too juicy of an entrypoint into the Arcology, he might deliberately leave it only lightly defended, so that anyone who got inside would get just far enough before Medusas, Blue Samurai, or even just Bumblebee drones/hives would take care of the intruders. Deus was incredibly devious and cunning like that, or at least that's how I always read into him.
And yeah, as Medicineman said, the UCAS military(and by extension Renraku in the local area) couldn't risk an all-out invasion, simply because the loss of life would be massive, and as a last-resort Deus could still overload the reactors in the sub-basement levels. And he absolutely would if he felt his defeat was imminent; Deus driving goal was to NEVER be captured and controlled by anyone again, even if that meant his own demise(though I imagine he'd plan for and attempt every other method to avoid that first). Or he could just use the obvious threat of killing every living civilian inside, and the UCAS wasn't willing to risk that either. This is getting a little off-topic, but my point is entry into the Arcology was essentially limited to surgical strikes and independent incursions by expendable assets(IE Shadowrunners). And knowing that, it wasn't the getting in that was difficult, it was surviving once inside that was...challenging.
Anyways, sorry for my tangent, but hope that lends some perspective.
