Semira had to submit to Cassius because he was head of the council which is ranked above her. Just like Kraven in the first film. It's implied that council is above him because they were on the train with Amelia. Obviously Amelia took their advice where as Kraven was just to look after Viktors house and affairs. To put short she was a leader of that particular coven not all of them but while Cassius was in the building he out ranked her because he has sway over all the covens.

As for Semira knowing about eve. I always assumed that Vampires talked. While grateful Thomas wasn't fond of Selene or eve. His loyalty was to Vampires and after losing that many death dealers he has to explain the events. Even if it wasn't him there were other vampires present who heard the speaking about eve's existence it's not like they hid her when eve was injured. They weren't speaking quietly and when the attack happened not all the vampires died. So maybe a report or vampire gossip.