Have you had your lunch?
Of course, this does NOT mean
have you ever had a lunch?
And of course, such a question is asked around lunch time (say from
11am to 4pm), when one is expected to have his lunch. Which means, of
course, that it's during all this period after breakfast, isn't it?
It's not a question about other days, it's a question about today. You
might have had or mightn't have had breakfast, though. Perhaps you're on an
empty stomach (you don't have money or time for breakfast) at the time of the question.
It means:
have you had lunch today, possibly since your last breakfast (if you had one)?