Vitamin D is produced in the skin, not the eyes.(1)

I would imagine that when those indigenous peoples were introduced to sunglasses, they were also introduced to a number of other items they had never previously known, such as tobacco, alcohol and fast food. Diseases they had no immunity to might also have played a role. The eyes have nothing to do with vitamin D production so blaming sunglasses is rather bizarre.

Vitamin D is produced in the skin, not the eyes.(1)

I would imagine that when those indigenous peoples were introduced to sunglasses, they were also introduced to a number of other items they had never previously known, such as tobacco, alcohol and fast food. Diseases they had no immunity to might also have played a role. 

The synthesis of vitamin D is well understood and sources describing it can be found in many places so I'm not going to quote the entire process, but a good explanation can be found here under the heading "PHOTOSYNTHESIS OF VITAMIN D". In short, it's a passive process that occurs in the skin and is not regulated by the brain, eyes, or other organs. What determines the amount of vitamin D synthesized by the body? Solely the amount of UVB photons penetrating the skin and the person's age:

Anything that either influences the number of solar UVB photons that penetrate the skin or alters the amount of 7-dehydrocholesterol in the skin influences the cutaneous production of vitamin D3. The amount of 7-dehydrocholesterol in the epidermis is relatively constant until later in life, when it begins to decline (17, 18). Ibid., "FACTORS THAT ALTER THE CUTANEOUS PRODUCTION OF VITAMIN D3"

There are no other factors mentioned in synthesis, and as you can see from the diagram here there is no involvement of the eyes or brain in vitamin D physiology at any point. Could there be an indirect involvement of the brain since it also controls the parathyroid glands? Yes, there could, but that wouldn't change the results of how we measure vitamin D levels.

Therefore, an assertion that the eyes are involved in vitamin D deficiencies is purely speculative and the burden of providing evidence for it would be on the person making the assertion. I can find no evidence to support the notion. It's also a little odd considering that a huge number of people living in developed countries have been wearing sunglasses for many decades without ill effect. Why would we have not seen this effect long ago? Is it possible these indigenous peoples have unique genetic differences that altered their basic mammalian vitamin D physiology and somehow caused their eyes to be involved? Well, anything's possible, but that would be an astonishing finding and it also is purely speculative.