Without disrespect, since your posts have been very helpful to me as a lurker (thanks btw), -1!
As a scientist (albeit in a totally different field) I feel that when people talk about variables in this manner they are misunderstanding the nature of different types of variables and the quality of different types of evidence.
I suspect wood age could well affect tone. And that the chemical/structural nature of the changes would in many cases be similar across a broad range of wood types - they're all lignin, cellulose, oils and water after all. Thus although the effect would not be constant it would certainly be similar and the trend would be towards a particular effect.
Wood age certainly improves the tone of acoustic guitars, that is generally accepted by musicians (who although not scientists do generally have the best, most discerning ear for their instruments) and by many makers I know of. Probably this effect has been examined in the scientific literature since it is commercially relevant though I don't fancy doing a search and review right now! People's experiences are worthwhile subject for discussion since they are the best type of evidence available in terms of audibility short of using measurement mics in an unfeasibly controlled experiment.
The 'thousand different woods and set-up' etc etc argument is used again and again on web fora as a 'myth debunking' argument, even in extreme cases I've seen on here to argue that wood type has no reproducible effect on electric bass/guitar tone, which is audibly and scientifically complete rubbish. It's a bit long-winded but I think it's worth going over why this is the case here. People forget that the resonance of the system AS A WHOLE is what gets amplified. The string/pickup coupling is the point at which the signal gets fed into the preamp but the string vibration will be damped to different degrees by whatever it's mounted to, ie the wooden body of the instrument via the bridge. In the case of wood type, these effects can be demonstrated to be audible by the performance of identically mounted strings of the same type set in tension within different wood types (via metal pegs if you like). Woods that vibrate to different degrees will dissipate string energy faster making the initial acoustic output louder and causing a faster global decay. It follows that resonance behaviour at multiple frequencies will damp different string harmonics to different degrees, hence changing tone.
Sorry if all that seems obvious, indeed first principles, but people often neglect it completely in these discussions! So on to wood age. Now, as people have pointed out the question is not so much whether there is a contribution as to whether that contribution is significant enough to be audible. It seems like these changes would be minute. Well, yes, but then so are the the rest of the signals we are amplifying. How small a change is audible after you've pumped it through a gain factor of say 100 or so? If you consider higher frequencies, where there is very little power, many many vibrations a second, and the ear is quite discerning, then relatively small changes compared to the fundamental are clearly audible on a clean enough system - think about how picky even moderate audio geeks are about midrange coloration in hifi systems. Changes in the moisture content of a system, or chemical changes to (for example) oils which affect chain packing density and flexibility are relatively big changes when it comes to resonance and stiffness characteristics.
So what about those infinite variation possibilities created by setup, different individual bits of wood, string age etc? Surely they'd dwarf any difference? Err, not really. There may be an infinite number of fractions between 0 and 1, but none of them are any more than 1! Each variable will have a characteristic range within which it acts, eg you can't duplicate the effect of new 50-110s by altering pickup/wood combinations on a knackered set of 45-95s. Similarly any chemical changes that wood undergoes are not going to be random, and are going to have an effect on the system over time that is not duplicable (sp?) elsewhere. Of course, it is technically possible for wood to both absorb and lose moisture over time but I'd imagine that in the vast majority of cases with guitars stored in homes they will lose moisture. Living wood is of course full of the stuff but even wood that has been seasoned for a while probably hasn't reached equilibrium throughout if it is a thick lump, diffusion rates through the material are going to be quite slow. This slow rate applies to air exposure of the material too, which as it dries out allowing access to (particularly) oxygen will lead to chemical changes. You only need to look at old timber beams in buildings to see how they blacken up and harden over the years! They do that irrespective of soot depositing.
Having very tediously said all that, I'm not actually sure if the age of wood does have a significant effect on tone. I just wanted to point out that it's perfectly possible that it does and that it would probably be largely consistent within a particular context. Whether it would be musical for a given guitar would depend on other factors, perhaps most significantly the wood type you started with and whether the change exaggerated or masked the particular desirable characteristics of that wood in the first place. Any changes would of course be more audible the cleaner your sound, as with pretty much anything else - if you have a dirty and/or effects-laden sound then even the wood and pickup type might be more or less immaterial!
Cheers all I hope that isn't too much a rehash of what's been said before.