Well he f**ked up seeing as Sin already has Gear powers, was brainwashed into fighting for Valentine, and...well, the red eye is on him. 3 chances for his cover to be blown, much less heavily scrutinized, on the chance a number people see what's going on and draw suspicion; one of which will, hilariously enough, have people peg Ky to be a Gear after all this time, putting his kingship and trust with Illirya in jeopardy.
And say that Sin only has that one red eye, because he doesn't have one on his left, that means he has heterochromia, meaning the red eye is inherently noticeable. It wouldn't be something that Ky can just turn on and off. And don't say he cloaked it because we don't know that either. Not to mention he has his own eyepatch which is much easier to cover up suspicion on its own.