Haven't watched the new series XD I can see Rex not knowing though. I can see not many of his kind knowing about it except for the higher ups.
Well, maybe she does get sick when scratched or bitten by them? That would make her think she's hallucinating with the fever and all. But the sickness like you said would oly last at most 24 hours, if not shorter. 
And maybe she has an alien form as well, except she's been cloaked as well. Maybe her mother was the one to design the first cloaking system and when she found out she was pregnant created a cloaking device of her own that was implanted under her skin, like a microchip? if not, than maybe just a piece of jewelry Cassie never takes off because she knew her mother gave it to her, like a bracelet or a necklace? or maybe she just has an alien form that she can switch too, but because she doesn't know about her being half alien, she has never switched to it before?