I understand ZUN is not out for money, but sometimes I ask myself: Would fans buy the game if he added another 1000 yen on top of it?
The percentage of anime fans that would buy non-pirate anime DVDs is quite low. Prices are the main reason, and because that fact is known to the anime companies, DVD availability is also low.
Given that only a handful of people don't care about money, if ZUN wants his stuff to be sold, he has to consider prices reasonable not to himself, but to the buyers. It's quite obvious that as prices rise, less people will buy. I'm sure ZUN, as well as all other doujin sellers, choose these relatively low prices so their works could be aimed at the general people without money (ie middle, high, college students).
I would think that people with limited cash would prioritize buying more products for more circles than less products for one circle (ZUN). Note that these other circles need not be Touhou-related.
For instance, if one Touhou shooter cost 2000 yen at festivity, 2100 at store, I'm sure most of those with limited cash would prioritize 2-4 favorited doujin circle CDs that cost 500-1000 yen each, assuming they don't use any source of piracy for the products they don't buy. The respect they have for each of those favorite doujin circles is the same as what they have for ZUN. Shanghai Alice Project is just one circle, even if it is the founder of one of the greatest doujin works in history. If they have limited cash, they would prioritize the less expensive. That way they can support more circles and get their hands on more products.
However, because ZUN's prices are reasonable, or rather, the same as all the other doujin circles, many would prioritize Shanghai Alice Project first. Explains why on the second day, 50% of the East side line would go to that one booth, and 90% of the West side line would go directly to the East side at opening.
I wouldn't really know, because I'm one of those people who never care about money. Just random speculation.