I see basically 2 explanations:
a) They just copied a list of organs from somewhere and didn't screen it further, ie, this is unintentional. Then again, while you could imagine a bunch of animators not knowing about obscure glands, you'd think they would have caught the eyes.
b) It's the prototype, we've seen that they had difficulty getting the EVAs into a proper humanoid shape, we've seen the misshapen limbs of the discarded prototypes, the next to the random number of eyes...
Maybe it wasn't supposed to grow those glands but the genes just got expressed.
Actually, you have all the genes for making both man and woman parts, what decides which you grow is a signal cascade started by a single gene on the Y chromosome. You can grow eggs from male stem cells and sperm from female ones (though sperm from reprogrammed woman cells would beget only daughters cause there is no Y chromosome) So it's probably a cell programming error.
Likewise, the second eye might be tiny and vestigial.
So without the helmet, zerogokis face looks like this:
Also the "unit zero" Fuyutsuki is shown in ep 21 is probably a different prototype that ended up on the EVA graveyard
Alas poor Kaworu! I knew him well...
- Essay on the character's roles in each others introspec sequences
- Good faith Analysis of Mari
- Finish ep 8 commentary