To get the meaning ' Hasn't he come until now ?' what should I ask 'Has he come yet ?or Hasn't he come yet?'
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In English, we normally form questions by reversing the natural subject / verb sequence of a statement...
John is here - statement
Is John here? - neutral question
But when the question includes negation...
Isn't John here? - "loaded" question
...this normally implies that the questioner expects / expected the underlying (positive) statement to be true. Including an adverbial element (such as yet, already) is irrelevant to this general principle.
Sometimes the negation might indicate surprise or annoyance - because the speaker already has reason to suspect that John isn't present, and seeks confirmation of this.
Other times it might be a "rhetorical" question - speaker suspects (or knows perfectly well) that John is present, and the expected answer is Yes...
Jack, will you please take out the garbage?
Isn't John here? - Jack knows/thinks John is present, and it's usually John's job to take it out
Has he come yet? - This is a simple question asking for straightforward information.
- Has he come yet? - Yes, he arrived 10 minutes ago.
Hasn't he come yet? - This can indicate frustration or impatience on the part of the speaker, or at least emphasize an expectation that the person should have come already.
I haven't seen him.
Hasn't he come yet?
Not yet. I presume he has been delayed.
Well, we'll have to start the meeting without him.