Apparently I should've clarified that when I said I would understand NXN implementing this at their national meet I meant that I would understand them implementing it at all of their meets (so the region meets as well). So states who allow middle schoolers to run varsity would not be able to bring those below 9th grade to the region or national meet until they are of age. Doesn't seem that outlandish to me, nor does it seem to be punishment to tell an 8th grader that has been racing with the team in NY all year that they don't get to go on and run at the regional and/or national high school meet until they are in 9th grade. They will still get 4 opportunities to do so.
That said, I don't have a huge issue with how it is done now, but I understand that gripe. Does it not make sense to limit competitors in a high school race to high school runners? Should they open it up to elementary school runners and college runners? While I know that sounds like an absurd stretch, I'd like to know why it seems reasonable to have a set cutoff as 7th - 12th grade for a high school race.
Unlike your area, we have middle school programs around where I live and they aren't allowed to compete in high school races - admittedly maybe that is shaping my opinion.
But you are right, Nike has little incentive right now to restrict it's allowed competitors. I doubt enough disenfranchised teams would boycott NXN to try to force change (and I'm not saying they should).