This is currently impossible to answer since the show deviates quite a bit from the books here.
In the books it goes like this (big spoilers for the books, not so much for the show since the final episode of season 2 already dropped the biggest spoiler of the books):
The biggest spoiler in the books being that Emhyr is Ciri's biological father and that this was the main reason Nilfgaard was searching for her all along. In the books, Emhyr keeps this to himself and nobody knows that Duny and Emhyr is the same person.
In the books, Geralt hired Codringher and Fenn. The "fake Ciri" was someone that Codringher and Fenn had found and planned to use to make the real Ciri safe from Nilfgaard's attempts. As it turned out, this served Vilgefortz's plans as well, so he had Codringher and Fenn assassinated to cover the tracks of the plot.
Emhyr sees through the decoy plot however and realizes that the woman sent wasn't the real Ciri. Publicly his reason for finding Ciri was to put an end to rebellions in Cintra and legalize his rule there. Secretly, he just wanted to find his daughter and keep her safe.
And so to keep the real Ciri safe, he marries the fake Ciri knowing she is fake. The decoy becomes Empress of Nilfgaard, in order to secure Cintra and keep the real Ciri safe both. Nobody knows she is fake but Emhyr, Geralt and the Lodge.
In the final chapters, Emhyr eventually sends Nilfgaard elite troops in order to save the real Ciri, although they arrive too late and Ciri has already been saved.
So in the books it makes perfect sense for Emhyr to marry the fake Ciri. The show deviates from the books a lot here and while it does, it doesn't make much sense at all... so there it is.