If you are already ready, I won't ask you to hurry up. I know you are not ready. For the same reason, I don't think you have been ready.
But I can still say I did in the past think that you would have been ready by now.
It's the immediate past that we're talking about here.
I thought, until a moment ago when I saw that you were not even close to being ready, that you would be ready by now ("by now" meaning at this point in time.) In other words, I'm surprised to find that you're not ready. I had an expectation that you would be ready and that expectation has not been met.
Let's say my wife and I were planning to go out and needed to leave at 7:20 to be on time. I walk into the bedroom at 7:18 and she's just stepping out of the shower. I say, "I thought (until I walked into the bedroom) that you would be ready by now (in order to leave the house at 7:20)."
Sorry to be so wordy, but I hope that helps to explain the thinking behind the phrase, at least as I see it.