Basically what happened was the result of a three year pattern and a change of ordering rules by the Mint in 1999. In 1999 the Mint thought there would be a tremendous demand for the proof sets with the new
State Quarters in them so they instituted a 2 set per household ordering limit. The price with all the new coins also went up. So no one, including dealers, was able to order a large number of sets. The order restriction also resulted in an initial shortage of sets in the marketplace. So what happened was the price of the 1999 sets went way up on the aftermarket.
After seeing the price increase and the profits that were made on the 1999 sets everyone was waiting for the 2000 sets to come out. But when they did the Mint had dropped the two set limit and everyone bought a bunch of sets to cash in. Of course this resulted in a glut of sets on the market and so naturally the dreamed of profits never occurred. So in 2001 when the sets went on sale people remembered that they didn't make money the previous year, and they were still sitting on sets, plus it was now the third year of the
State Quarters and the novelty was wearing off so people just ordered what they needed, not extras and the total number of sets ordered went way down, even less than the 1999's. And when that was noticed they exploded on the aftermarket.
But is the high prices for the 99 and 01 sets justified? Not if you compare the mintages to earlier years or even later years. Their "low" mintages really aren't really that low and several "common" sets from the 90's have lower mintages. The high price of those sets is still just a holdover fro the speculation of the time. Eventually I would expect the prices to drop back down close to the normal prices for the surrounding years. Because of their reputation as being the key date years I would expect them to stay a few dollars above their neighbors but eventually not more than about 10% higher.