That probably has more to do with the fact that JKA and JK2 are over 15 years old now, the only ones buying it would be the old fans. There is no real reason to make a large stock when most of the current player base is pretty low . The people who just want to try the game will get regular copies most likely.
Even then, 1,000 copies only is still ridiculously low. Also, I think you underestimate the popularity of JK2/3. They weren't obscure games at all. lol
Then that's probably what's gonna happen here, I think the aim is more to sell the regular new editions of the games for the different platforms. This seems more like the publisher is not really interested in putting money towards those limited editions, and just puts out a really low number as a marketing tactic so they will all sell pretty fast and leave people wanting more. It will likely boost sales for the regular editions.
To add insult to injury, alot of resellers likely brought them too. You'll be able to find them on ebay for massive markups, which is abit of shame