@Denis and Pjotr:
This question is more about the official registration in the register, than about the linguistic correctness of the translation. If shipping company and authority put down the ship name "Estonia" in the ship register, it's the officially correct translation for this ship.

Also, it should have been "YEkaterina II".

I'm agreed with Pjotr here.
One of the many cases when name via correct transliteration is different from that on the nameplate. Anyone knows why this happens?

The name which is shown on the nameplate beneath the funnel says "Estonia"

The correct name must be Estoniya, because Russian А=A, but Я=YA, thanks