Debian decides to allow secret votes

That's already how NOTA works, more or less. If you rank it above a choice, you are approving of that choice. If you rank it below that choice, then you are disapproving of that choice. Most of the time, a choice only needs simple majority approval by this method, but constitutional changes require a 2/3 supermajority.

In this case, it appears that some voters ranked Option 3 over Option 2, but then also approved of Option 2. You may believe* that is an illogical vote to cast, but it is a valid vote, and in a democratic system, we generally presume that valid votes should be counted even if we think they are illogical.

* It might be the case, for example, that some of these voters wanted Option 2 to lose, but did not want it to lose by failing to get a supermajority, because this would be perceived as a "tyranny of the minority" situation, and so they would prefer the lesser evil of Option 2 winning.

Why didn't they just do that in the first place? Vote 3-NOTA-2. We must assume they had a reason. There is no need to further complicate the ballot with additional requirements when the current ballot suffices to express that anyways.

And as this very debate illustrates, there is no such consensus.

To "accept" the result with the proviso that one can then simply relitigate it is to evade the fundamental point: the litigation then requires a 3-1 majority *the other way* to return the status quo ante.

The smugness of those defending the sanctity of process here is rather difficult to take.

I am very disappointed in the Debian leadership and frankly for the significant section of its membership who are moving away from the transparency, not only at the aggregate level, but the individual, which I always thought was one of its many core features.

No. These rules are for humans, not machines, and it doesn't work that way. There is already lots of ambiguity, loopholes and ways to twist most rules meant for humans, and then you can claim you are following them to the letter. In the same thread about this, someone pointed out a constitutional change that was voted on years before but never implemented. So, there were already rules that were being followed to the letter with the opposite intended result.