As far as an overall decrease in height over the millennia between the War of Wrath and the War of the Rings goes--a period of seven thousand years, and close to as long as the Hobbits had to diverge significantly from their initial Mannish stock--is it not possible that the Orks became shorter as a result of evolution? After all, they survived the end of the First Age chiefly in dark hiding places, that is to say caves and such, and these remained their chief dwellings into the early First Age and beyond--Mordor and Isengard notwithstanding.
After all, if the Orkish breeding stock after 1 S.A. was to be found only in those Orks that made it off Beleriand and into the mountains somewhere (and presumably the Blue Mountains were a bad bet, given all those Elves, Dwarves, and Edain swarming about), wouldn't it make sense that almost all of the ancestors of the much-later Third Age Orks would have been, typically, the smallest specimens of Ork: those most suited to an underground life? What's more, barring the realm of Sauron in Mordor (which was not a constant for every century, and which still had to deal with daylight), smaller Orks would have been optimal for surviving in conditions such as those seen under the Great Goblin.
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I prefer history, true or feigned.
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