Back in the day (60's,70's and early 80's) Daytona's weren't that popular. However something changed. Rolex made fewer of them, the SS Daytona became harder to get, Jewelers could only get a few every year, they grew in popularity, and soon there were waiting lists. Thus those who bought more at their Jeweler were those who went to the top of the list. Like already said you could pay MSRP and walk out of the store and resell it for a very handsome profit if that was your wish.
However with the combination of the economic downturn,the cost being quite a bit higher, it appears as the boom years maybe over. However jewlers can still only get so many SS Daytona's every year and there are still some areas were it is pretty difficult to get a SS Daytona. However to this day I have yet to see a brand new SS Daytona being displayed in a Jewelers display case. They are usually kept in the back in the safe. The same cannot be said for the Gold or SS Daytona's. The Gold ones cost much more and are much easier to get because Rolex doesn't limit Jewlers ability to get these and not that many people can afford them. The TT which cost more than the SS aren't as popular and are pretty easy to get as well.
Patek also does the same thing with their 5711 Nautilus and Aquanaut. Patek does not over produce these watches and they are not as easy to get as a number of their other watches in the 20,000 to 100,000 price range. You would actually would find it much easier to buy one of their 85,000 watches. For them it makes a lot of sense. By doing so they don't cheapen the brand buy making it so easy to get a Patek (cost wise) and they keep some of their less expensive watches special.
In the 1960s', 70's and up through the mid 80's most dealers couldn't give away Daytonas. In 1984 it also seemed the Sub and GMT were the top of the line SS watches as they had MSRPs of around $1,350 and a Daytona was only $1,100. Daytonas were often sold at very large discounts. The original Daytonas were manual wind and the steel models were not certified chronometers. Those were 2 issues that back in the day hurt its sales as most people thought of Rolex as being synonomous with automatic movements and some people thought a certified chronometer means more than it does today. Many people say the Italian collectors were the first to start to become interested in manual wind Daytonas. Some people have said it was the result of people seeing Paul Newman wearing a manual wind Daytona, in a film. Not sure how true that is as I've never seen footage of him wearing one in a film, although there are several pix of Mr. Newman wearing different Daytonas over the years in his personal life and as a race car driver. In any event, I think the second generation Daytona, which had an automatic movement truly changed the Daytona market and it quickly became one of the most sought after watches. Rolex also increased its price beyond that of Subs and GMTs. When I first became interested in the early 90s they had a list price of around $3,850 (Subs and GMTs were around $2,850). Supply seemed very limited as they were only getting a limited number of movements from Zenith, and they seemed to prefer to put them in the newly released two tone models, or the all gold models since the profit margin was much higher on those pieces. I believe the shortage of the then new automatic Daytona caused people to go back and buy manual wind models, which eventually surpassed the value of the automatic watches. The market on Daytonas definitely became softer with the economy colapsing around 2008 and prices of SS Daytonas hitting $9,500.