I understand "Will you not smoke?" as meaning I am smoking, others are smoking but I wonder why you are not because I thought you would smoke also. So in a way I'm asking you to negate my question. "Could/would you please not smoke." is the request to stop smoking.

Allen, The problem with your sentence is that you are using an older definition of the verb "will". A long time ago people used the verb will to express WANT and desire. Twelfth Night, or what you will.......a Shakespeare title Love God and do as you will......St. Augustine. The expression "what you will" is still in use today. It means "what you want". Say what you will about education, it is still very important. Go ahead and take what you will from me. It doesn’t matter. Although you can still use "will" to express a polite request, you have to be careful when using it in negative sentences. Will you help me? .....this is easy to understand as "Do you want to help me?” But in a negative sentence it could be interpreted like this: -Will you not smoke? = Why don't you WANT to smoke? You would have to say it like this if you are making a request NOT to smoke: -Will you NOT smoke?...putting stress on the word NOT when you say it. Will you please not smoke?....This variation makes it clear that it is a request not to smoke. Won't you smoke? ...could be interpreted as ......Don't you want to smoke?

I think that your first variant is correct. It is a polite way of asking a person to stop smoking (at the moment, not in general).

"Do you want to smoke? " is asking you whether you want to smoke and is giving you permission to do so.