That wasn't Koto that Shisui used on Danzo. It was a regular Sharingan genjutsu.
OT: I think it depends on the eye. Shisui's left eye, which Danzo had, was shown to be able to actively mind-control a particular target, and like regular genjutsu, it can be detected and canceled if the person being affected is made aware of it.
Shisui's right eye, which Itachi had, seemed to be able to use Koto in a way that it affected the target immediately with a specific directive ("Protect Konoha", in the case of Itachi's one use) and had a lasting, permanent effect on the target's mind and behavior. That doesn't seem like something that can be countered or negated, because the jutsu itself isn't lasting, but the effect it has on the target is. It broke Kabuto's control over Itachi, and Itachi believed it would be enough to convince Sasuke to "protect Konoha" without him even being alive or present to witness its use.
So, Shisui's left eye controls your mind, and Shisui's right eye changes your mind, to my understanding. Logically, Shisui with both eyes would be able to do both at once, and be much more powerful than either eye individually, so it's hard to say, but by feats, the left eye (active ability; less powerful) has been countered, the right eye (triggered ability; more powerful), hasn't.