Ofc Minato wouldn't know of shishui's eyes or its capabilities , he died a long time ago before shishui was an adult, and Kotoamatsuki does not require eye contact, For eg- Danzo's eye was covered with a bandage and he casted it on Mifune during the Kage summit
You maybe be right about that but until proven, we can say that Minato can't be trapped by a genjutsu. Take his fight with Tobi as an example. Why would a proficient genjutsu user like Tobi failed to use his sharingan on Minato? He failed not once but many times. He was planning to destroy Konoha but why didn't he use his advantage? It doesn't make sense.
Tobi failed to use his sharingan before the battle, during the battle, and after the battle. He took naruto as a hostage the 1st time they met. It doesn't make sense why he was unable to use genjutsu when all he wants is konoha's destruction. He could put Minato in a genjutsu like what he did to Yagura and the fox and order him to destroy the village.
Tobi was able to control the fox and yagura (one of the few people mentioned by Danzo to have achieved full control over their respective beast). From these feats, we can say that Tobi is a proficient genjutsu user. It was said that Madara uses his EMS to control the fox. Tobi was able to control the fox. What does this mean?
The most logical reason I can think of why Tobi failed to use genjutsu on Minato is that Minato can't be controlled by a genjutsu. I am speculating but in the most logical way. I don't count KA as an immediate win for Danzo.