I think there's two different scenarios playing out here that need to be addressed separately, namely how many entries the competition can handle (regardless of how many individual entrants there are), and how many people can effectively get into the system to get an entry established.
There are many good reasons why the competition is limited and have been outlined and primarily seems to boil down to available resources, time and money to handle such an event. You may want to consider allowing a small overage this year as I will comment in a moment.
Getting into the competition is a whole other situation. Where I am concerned is that the entry system is flawed and whether someone had 1 or 15 entries, they may not have the same opportunity to enter this year. From the current comments on the entry site pages "Unpaid entries in judge centers that have reached the capacity limit for paid entries will be reassigned to an alternate region" and " Rest assured that all currently registered entries will have an opportunity to be judged in the competition." So, are those folks that registered over the available amounts going to replace the available spots in other regions that were not full? I was in the midst of entering my information, but not to the point of getting a beer entered when entries were shut down by the AHA. So who gets to enter at that location now, someone who through no fault of his own was able to enter above and beyond the capacity of a location, or someone who was unable to complete registration not because a site was full, but because it was determined to suspend entries? I don't buy the argument in this situation to get online earlier and enter earlier in the day, otherwise you should make the entry period from 1-4pm regardless. Oh, did I mention that the email with the link to the entry sites didn't hit my inbox until 5PM? I didn't personally have info to register until hours into it, and my primary location was overbooked but felt fortunate to get into another one. This registration was flawed from the beginning.
Some posts have promoted or countered the concept of a lottery. How is the current system so different from a lottery? How many people hit F5 hoping to "get picked" so to speak to get into the server? How about those folks who punched their ticket by being able to register above the available spots in their region now taking spots from other regions? Luck of the draw for those who got in and registered above a regions availability, bad luck for those in available regions who now lose their spots in that lottery.
I surely don't know how to fix that, but will feel like I won my own personal Ninkasi if I manage to get an entry in this year. Obviously, this will not be a year where anyone can win - those who were lucky enough to bypass entry limits have a edge over others who otherwise would have got an entry in. In essence, some of us are already winning an unofficial lottery to get in, so would that be a terribly bad way to do this? At least it would be an open lottery, and not closed to the luck few who got picked by the fortune of getting in at the right time.
If the judging sites can handle a few extra entries, a feasible solution to the overage would be to allow the regions fill naturally when the sites are reopened, then redistribute the entries that got in over a region's allotted amount. That will make this years competition go over the 8250 mark, probably add what 50 or so beers to each judging site, but would solve the dilemma how to keep those in that over registered in say NY because of technicalities, but not punish those entering in say WI where there was still room because the AHA shut the site down early.