I've read it somewhere a long time ago, in some interview with some of the original creators who worked on the game around the time of it's launch that AO was originally meant to be a whole lot different game than what it turned into during the development process (and I think there also was some redeisgn involved).
It was to be a heavily PvP focused game about two warring factions that try to gain control over the gameworld through a mechanism similar to the current tower wars. There was to be only a minimalistic story involved and the game was planned to be perodically "reset" (or only have a very limited planned lifespan/runtime) once one faction or the other gains ultimate superiority.
The name "Anarchy Online" was to reflect this fierce and somewhat chaotic battle fought over the control of the land without any rule but one: destroy the opposition.
The way I see it, everything Omni-Tek (including its earlier incarnations, whatever their names may have been) does is in some way originates from the Omega, and what they do is suggested by those of the Unredeemed (or the Braces they worship, or whoever Vanya and Co. actually are) who manipulate/control them.
The Omegas themselves may not always have all the information about why they "should" do what they are "suggested" to do, but those who make those "suggestions" to them know a lot more about a lof of things.
And Omni-Tek was built exactly to be controlled like this, to provide total control over the employees, to ensure their unconditional loyalty and to make sure they don't ask questions, don't think about the orders they are given, they just do as they are told. And when your people are trained out of asking the wrong questions, or any kind of questions for that matter, you don't really have to make an effort to keep things in secret as there won't be anyone who you need to keep those things secret from.