[spoiler]Cubia definitely was an anti-hacker program. In fact, here is the entire description of Cubia, verbatim, from the fourth //Liminality disk.
Morganna could anticipate human behavior and plan ahead. One example of this was Cubia, a monster designed to balance the game against hackers and edited character data.
Cubia was meant to seek out malicious players with illegal abilities or items like the Bracelet and Data Drain them, deleting their PC files. Until Kite received the "Book of Twilight" and the Bracelet, no players fitting this description had appeared, so Cubia had not been seen. Once the Bracelet became active, Cubia sought Kite whenever he came in contact with Aura, because it believed Kite was a threat to the system, to which Aura belonged. Cubia did not attempt to attack Aura or the malfunctioning Morganna because it saw both Morganna and Aura as parts of the game world.
Cubia disappeared when Kite destroyed the Bracelet because the danger to the system was removed and its job was done. Cubia remains in the system, however, and should something new appear that threatens game balance it will launch again. Cubia adopted Kite's character data every time that it was launched and was able to keep pace with Kite's increasing powers.
On this //Liminality disk there is an easter egg that explains what all the phases were originally before Morganna corrupted them and other little goodies. So if you want you can check yourself to see all the different descriptions.
Now as to why it never attacked Helba...I have no idea why it didn't and that is something that I have questioned myself. As you can see in the description of Cubia, it is suppose to go after hackers and other malicious players, but for some reason it only attacks Kite and it was first activated when Kite gained the Twilight Bracelet. Kite having the bracelet had an enormous amount of power to wreak havoc in "The World". As Aura said, it can bring either salvation or destruction at the whim of the user. Having such an item as the Twilight Bracelet is why Kite was being attacked and why Cubia was activated. As powerful as Helba was, she simply did not have that sort of power, and that is why she wasn't attacked.[/spoiler]
That is the only explanation that I can come up with.