If the lottery results in some people having more opportunities to enter beers then that has a big impact on who can win ninkasi. I have to imagine few people really enter with the expectation of competing for the ninkasi but if you were one with that goal it would really suck to pull a low number in the lottery.
Why not treat the NHC as sort of the playoffs of homebrewing competitions? Rather than make it an open competition, set a requirement that beers can only be entered if they have scored a minimum score in one or more AHA-sanctioned competitions. It shouldn't be that hard to coordinate a database of results from sanctioned local competitions. The cutoffs could be set to allow the maximum number of beers the AHA can support appearing at the NHC. In the alternative you could require a beer to pick up a designated number of points to qualify where points are earned based on scores at sanctioned competitions. If necessary, the local clubs could be required to pay back a flat amount or portion of entry fees in exchange for becoming a qualifying event.
It's win-win. It focuses entries towards local competitions where brewers are more likely to get detailed notes. It also cuts out low scoring beers from the NHC infrastructure, which opens more spots for quality beers. Honestly, there is no reason for beers below 35 points being judged at the NHC.
I disagree wholeheartedly with having to pre-qualify for this competition. NHC should be about inclusion. There is perfectly fine competition called MCAB, Master Championship of Amatuer Brewing, that does just what you describe above. If this is what you strive for then target your entries toward that competition. Any AHA member should have an equal chance to enter at least one beer into NHC. After that every member should have an equal chance to enter a second beer. I am glad that they have instituted this sort of "pre-registration" that 1) gauges the interest of all the members and 2) eliminates the need to register at one particular time during the middle of a workday. If there are more entrants than entries then good luck with the lottery. I hope they do the lottery the right way, and only institute it if it is needed (more entrants than entries).