In Man of Steel; How is it that no one seems to know of Lara's Pregnancy? Did Jor El hide her away for the entire term of her pregnancy? Why was it considered Heresy?
Well, we can presume that they could have hidden her by reducing the number of public appearances, a clever use of robes, seclusion(you can see that their home is kind of secluded) and not staying exactly in the city.
To answer why Zod proclaimed it to be a heresy, please understand, that Kyptonian culture had come to endorse, proclaim and follow the artificial birth culture, where every child created was done so for a very specific purpose. That child did not have any choice, or any say, and the shape of society was in the hands of the rulers who created them. To have a natural birth was to challenge the rulers and their system of artificial birth. By being naturally born, as Jor-El put it, He can choose what he becomes. He is free. Therefore, his presence and birth in society is against the rules which proclaim that every man is born for a very specific duty chosen for him even before his birth. Hence the shock and proclamation of heresy
We're not really shown her carrying Clark to term, just him in the ship.
We can make assumptions though. Jor-El was a rather smart cookie, so he probably figured out a way to hide her away or figured out something to hide her belly (assuming they get pregnant like humans).
Also, from what it sounds Kryptonians weren't used to women walking around pregnant, so many of them probably wouldn't have known.
If Kryptonians can make fabrics resistant to fire, bullets, weaponry, one would speculate they had technology to make any figure appear svelte. Probably Jor-El tailored a suit for Lara that hid her pregnancy.
Why heresy? Eugenics was probably a law.
Natural birth is always unpredictable. Krypton was so advanced that they could control any outcome and they wanted control every Kryptonian's destiny.