Why is it wrong if you write "onko nyt siisti?"
You can only rarely leave out 3rd person singular (hän, se) and plural (he, ne) pronouns, and in this case the sentence doesn't really work without a pronoun. You could just as well ask "Onko hän nyt siisti?" without the verb changing.
Onko se siisti nyt? Should also be a correct answer.
Be understood you will, but sounding like Yoda you will too.
Well, in this case I think it works just as well as the example translation. The emphasis is just slightly different. :)