"Well that is something you should take up with Mister Spock. I'm not in a position to start rearranging the furniture in your shower."

At the very least, she's glad that they can joke after walking through absolute hell in Zompania. Which was all she was doing-- the flirting, Kirk would have realized, would have been met with Vastra's unflinching ridicule. So it was probably a good thing that he was too tired to think of anything.