I can agree that the Valar choosing to completely destroy Numenor (given Tolkien’s assertion in the Letters that the power to do so came from Eru, but the Valar chose the method of wielding it) does seem like overkill, but I’ve generally just shrugged because Tolkien wanted his Atlantis. (I mean really the Numenorean fleet was not a substantial threat, just destroy the fleet and leave the island alone, that’ll probably take out the leaders anyway.) However, the Valar are as a rule not the type to take that sort of aggressive action. Even leaving aside that I firmly believe the Valar to be fair and just rulers, I just can’t think of any other time they take action that abruptly and dramatically. That leaves the question of why, exactly, the Valar chose to wipe out Numenor, and particularly in that specific and dramatic a fashion.
The question of why exactly Numenoreans/Dunedain are so wildly different from regular humans – practically half-elves. @anghraine‘s posts about Numenoreans as parallels to orcs here and here* seemed close, but not quite right, the orcs required a lot of hands-on intervention while the Valar seem to have been pretty hands-off w/r/t Numenor, and it doesn’t really explain the variance in lifespan we see with later descendants of Numenor or the general waning lifespan over the history of Numenor. Orcs stay orcs, but Numenoreans start losing some (some! not all) of their elvishness just from turning away from the Valar, even without the genetic dilution that happens in Middle-earth. (Other aspects seem to be stable traits that don’t need maintenance, so to speak.)**
Valinor is what it is – deathless, holy, preserving various species that are extinct elsewhere, etc. – due to the presence of the Valar and not of it’s own nature by right. We know that Melkor dissipated a great deal of his power by sinking it into Middle-earth in order to contaminate and control as much of the land as he could. So it seems self-evident that a great deal of Valinor’s character is due to the Valar’s power having rooted there in the same way, though less-intentionally, and to a much lesser degree on an individual basis. Each of the fourteen Valar sinking a small fraction of their power into Valinor could easily have a cumulative effect just as substantial (if not more so) than Melkor’s influence on Middle-earth. Or, thinking about it from another angle – the Valar (and their Maiar) on some fundamental level are the spiritual manifestation of the [meta-]physical universe itself. I.e. we know their visible forms are just constructs they use to interact with the embodied races; their ‘true bodies’ are in a sense the physical and metaphysical matter which they are responsible for. So Melkor’s contamination of Middle-earth is at once a direct conflict with them over territory, a way of taking control of some portion of them, and an indirect method of poisoning their very nature both by metaphysical contamination and by forcing them to make no-win choices where every possible outcome makes them complicit in death, destruction, pain, despair – the Trolley Problem writ large, only Melkor is driving the trolley while the Valar can only control the tracks.
In the Athrabeth, there’s discussion of whether the race of Men in their current state exist as they should and/or what influence Melkor has had on Men since he discovered them before the Valar did and thus had a chance to poison them unopposed. There’s a school of thought that says Men were originally immortal.
All this taken together, my conclusions are:
The Numenoreans were not in fact orcs, but rather the reverse of orcs. Numenor was land untainted by Morgoth’s influence, defended by the purifying nature of the Sea. The people there were able to live free of Morgoth’s corrupting influence, spiritually and physically. However, they still brought with them the effects of Morgoth’s direct corruption of their ancestors and the secondhand effects of living in corrupted territory. (This was also one of the forces behind the Curse of the Noldor, in addition to the Middle-earth equivalent of karmic retribution.) Numenorean traditions of showing reverence for the Valar were in part a ritualized way of giving affirmative consent for the Valar to intervene in their lives in order to ameliorate the effects of Morgoth’s corruption and restore the Numenoreans to the original state of humanity. For example, it would be reasonable that due to his fear of Men, Morgoth nullified their psychic/’magical’ capabilities as much as possible, and that the Valar managed to unlock those abilities again for the Numenoreans and their descendants. While some of these interventions were permanent and stable, others were less-so. Aging and sickness in particular were more complex problems which the Valar were able to only mitigate and not completely solve, so that once the Numenoreans began refusing the influence of the Valar (by no longer affirming their consent to Valarin influence) the effects of the mitigating influence of the Valar began to dissipate. Height would be a similar thing – it’s well established that malnutrition, stress, etc. in adolescence have a direct impact on adult height, so without the Valar defending the Numenoreans against the physical and metaphysical stresses of Morgoth’s pollution, the average height in the population again decreases.
Note that the Valar don’t do anything at this point, although they are probably saddened to see it happen, and worried about future results. (Rightly, as it will prove.) The Numenoreans have always had the right to withdraw their consent to direct Valarin influence. The consequences of so doing are not a punishment, but a return to some aspects of the prior status quo. The Valar cannot do anything about this without breaking their own moral and ethical standards, and thus corrupting their own nature by so doing, with very real and substantive impact on the balance of the universe itself.
Then Ar-Pharazon brings Sauron back to Numenor, and now the Valar start discussing direct intervention. As one of the Ainur, Sauron has a much more direct understanding of what the Valar did in creating Numenor. He takes full advantage of residing in an outpost of the Valar’s power that is inhabited by people who have become hostile to the Valar to begin actively corrupting the metaphysical nature of Numenor rather than passively eroding it as the Numenoreans had been. This is the point of all the human sacrifices, especially of the Faithful. It’s not actually going to do anything about Morgoth being shut behind the Doors of Night – but it will actively extend Morgoth’s corruption of Middle-earth to Valinor, further damaging the Valar and their Maiar. It’s a direct assault against the Valar and the sanctity of Valinor, especially since there’s direct travel between Valinor and Numenor. Destroying Numenor becomes a serious consideration, for the same reason that a gangrenous limb would need to be amputated. However, the Valar do not have direct authority over Men, and cannot force an evacuation of Numenor before they destroy it, so they hesitate. (Again with putting the Valar in the position of having to solve the Trolley Problem.) The attempted invasion of Valinor by Sauron and Ar-Pharazon is the point at which the threat is no longer contained (the gangrene is now turning septic, to extend the metaphor) and the Valar are forced to take action. They appeal to Eru and receive the power and authority to destroy Numenor (purifying it in the process), put Pharazon’s fleet in permanent quarantine/containment, and remove Valinor from the circles of the world so that it can no longer be directly threatened, now that Men have proven themselves to be a potential threat undeterred by the Sea (unlike Morgoth). No one is happy about this outcome.