Did the Emperor not know that Alpharius / Omegon were twins?

[Valkia the Bloody]

I am making my way through a re-listen to the Horus Heresy audiobooks (and also listening to some of the books I have not read before).

I just finished the First Heretic. 

One thing that has vexed me years ago when the book came out, and is now vexing me again, is the scene of Argel Tal looking at the Primarch pod of the Alpha Legion and seeing the twins. 

In some of the later Horus Heresy books, as well as the Alpharius novel, it seems to be a massive secret that there were twins. 

For example, in Pretorian of Dorn, the Imperial defenders do not know about the twins. 

It just makes no sense to me.

Does the Emperor not have eyes in his head? Did the Emperor know but not tell anyone as some kind of in-joke and later forgot for some reason?

Did none of his breeding science minions realize that one of the Primarch pods needed twice the nutrients and produced twice the waste? Or were they not fed because space-magic? Or are Primarchs like ant larvae that do not produce waste and store it in a sack inside the body until they are born?

Did they fire the wet-nurse before she could spill the beans?

What is going on here? 

Please enlighten me.