I would never want to discourage question-asking, especially when she's questioning things that can be pretty habitual and mundane and those are sometimes the best things to question. That being said, I can see how it would drive you insane!
Your exchange with her about lunch had me laughing out loud. It had a "Who's On First?" quality to it. :-)
She's got some great questions, though. Maybe she's searching for the arbitrary, sensing things that don't make sense. What if you just said "Lunch is ready" and then sat down without another word, and began to eat. Would she have joined you? Would "Lunch is ready" have generated a "Why?" from her?
Maybe she was pushing back because you were stating things that were your opinion, and I bet anything she was pushing against them to see if they were really facts....
For example, "Lunch is ready" is a fact. And she can see with her eyes that you are sitting at the table and that there's a place set for her there. Without saying more, you could just trust her to join you.
You said " It's lunch time, your food is ready, and when we are eating we sit at the table so we don't make a mess." She asked Why because "we sit at the table so we don't make a mess" is actually probably what YOU do. On the other hand, SHE probably sits at the table because you tell her to. So she could have perceived your statement as question-worthy for that reason. (As in she could be thinking "it's not why WE sit at the table mom--speak for yourself!") She might have said that she doesn't like to clean up messes, but I have my theory on that (see below). But have you considered that kids aren't as mess-averse as we are? Cleaning up messes can be a chance for them to show mastery. When there's a spill, saying "whoops, there's the milk" and wordlessly handing her a sponge (withOUT a command to clean it up) can be a task some kids don't mind at all. In fact they might actually feel like a real grownup when they are allowed to see the problem and take action to solve it. It's we grownups who tack all the baggage onto cleanups.
You said " It's easier to not make a mess, then we don't have to clean it up" - again, your opinion. I'm not trying to be mean, here. I truly believe that's an opinion. A value judgment.
I maintain that her "no" at the end (about cleaning up messes) was the result of what they call "leading the witness" in TV courtroom shows.
This last one, halfway through lunch "Mommy, why do we have to sit at the table for lunch?"
could have been marvelously answered with. "We don't! Let's sit on the floor." Grab 2 towels out of the linen closet and down you both go onto the floor for a picnic! She would have probably been DELIGHTED and you two could have shared a scandalously "improper" moment together. :-)
I'm not criticizing. I'm just saying that kids have awesome BS detectors, and so much of what we parents say is, unfortunately, often BS. Not intentionally, but because we're tired, we're on autopilot, it's what we've always done, it's what our parents taught us…..all that. But it's BS anyway.
I think that one should never give the kid the impression that asking questions is yell-worthy. Tempting, yes, but you do NOT want her growing up, afraid to question what she sees as silly or arbitrary. But again, there's a time and a place for everything. You don't want her raising her hand in church and saying "Hey Reverend Smith, that stuff just sounds like make-believe!" She can learn to hold her questions until an appropriate time. So if she's making you nuts and you don't have a ton of time , instead of reacting negatively to her questioning, just honor her questions but tell her you can answer later (pick a time). And if she says "Why" to THAT…..you've already answered and are under no obligation to answer further. She will learn your boundaries in that regard.
Does that make sense?
So to answer your original question about what to do, I'd suggest trying to find out what she is REALLY asking, and answer that. Perhaps if she felt heard in that way, maybe the endless stream of Whys would slow down a bit. :-)