I havent played any true vintage intruments but I have also wondered at their merit and desirability.
I think there are a number of reason typically given, and my feeling is that today, a vintage sounding electric guitar can be made if one is willing to pay a little extra/or the manufacturer has the skills and materials to do so.
Aging of wood making it drier and more resonant? Top brands and guitar models use select wood which is also "aged" in special ovens to replicate this process. Obviously true acoustic instruments would be more greatly affected.
Various alloys and ceramics used in pickup magnet manufacturing can also give an aged magnet sound to mellow out the pickups such as the various alnico magnets.
As for the vintage instruments themselves, as already pointed out, not all vintage instruments (ie year of manufacture) are equally sought after. The 1950's era Fenders and Gibsons are by far the most sought after AFAIK. I think there could perhaps be some luthier skills to attribute for this (eg, the CBS-era Fenders were not highly regarded), and I think a fair amount of it is just antique prestige value of the instrument.
In the case of the new Eric Johnson signature strat, which is praised for its vintage-like sound based on a 1957 strat Eric plays, it is largely attributed to its select grade lightweight alder and the nitrocellulose finish on the body and neck. Nitrocellulose finish on Fenders were more common in the early period and being a thinner porous coating material, it allowed the guitar to retain more of its natural resonant/harmonic qualities, more so that the thicker and durable polyurethane finishes used in most guitars today. Earlier Fenders also had thicker (smaller radius) necks, which add to the tone. Todays Fenders have different radii necks available and I dont think the smaller radius ones are as popular because of playing difficulty.
Today, the original luthiers from Gibson who did not wish to move from their original Kalamazoo, Michigan location, continue to build guitars under the Heritage brand, which are arguably of an higher quality than instruments that Gibson is making today.
So I think the vintage guitar desirablity is a combination of reasons, but I think a modern instrument can be made with a vintage tone if the right materials and lutheiring skills are used IMHO.
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