Ash,
Great topic that deserves a response, given we can blather on about Finnish hockey for several posts!
I guess you would say I start with some scientific measurements, consider ingwind when creating fw width, but then finish the design intuitively.
I find out from historical weather data (now easily available on the internet) the average and gust wind speeds of a site, typical directions in different seasons, etc. I consider a base fw width to be 30-40 yards, depending on the length of hole, and consider widening it for windy conditions. If average crosswind speed is 17MPH, I might widen it 17%, if 36MPH, then maybe 36%. I don't know if there is specific correlation to how wind affects any given ball, but think this is generally a good start.
In general, if a hole normally plays in a crosswind, I add some width to what it might otherwise be. If in a headwind, I add a smaller fraction, and if its downwind, I may narrow it. I also widen fairways if there is a substantial hazard like OB or water on one side, esp. if on the downwind side, or there is crossslope.
Of course, I also walk the hole after clearing to see if it really feels that windy, what the hole calls for, what trees or features to use/preserve, etc. Open sites need this wind consideration more than ones with mature trees, which block wind, or sometimes make it swirl.
The goal is to avoid a fairway where typical conditions make it nearly impossible to hit with a reasonably good tee shot. Now, I don't want all tee shots to come out about the same difficulty level, and don't mind a tough tee shot. I narrow one long par 4 every course for difficulty, for example. But, I don't want them to be impossible.