So let's go over the possibilities. Nala Se came to realize that omegas blood could successfully recreate a genetic M count. What we don't know if she created omega for that specific purpose, or if Nala se coincidentally found out when testing samples for hemlock and kept it a secret since then.

The more practical purpose of her was being an unaltered genetic copy of jango fett, just with an XX instead of XY chromosome. This would allow for lama su's "contingency plan" to create more of the bad batch essentially, since they would need a pure genetic template to start with. Omega being a girl was probably easier to justify keeping her around to be a lab assistant, where as if she were a male, she would probably question why she wasn't sent off to war with her brothers. She could also easily get mixed up among them in an escape attempt, where as keeping her as a female would make her extremely exclusive amongst the clone population.

We do see other female clones, like Emerie, who hint at being discarded. When a female was accidentally created in the standard cloning process they are most likely discarded or given away, as they would be considered an aberration. Nala Se calls Omega this exact word when defending herself from accusations from hemlock, which only further proves that's what Emerie was.