I forgot this topic existed. Personally, I think the eye is a symbol of perception and the ability to gather hidden knowledge, particularly magic. The open eye has been used for centuries as a symbol of awakening to higher knowledge or inner vision. It's use on items such as the Lens of Truth invoke this symbolism, while for mage enemies it may just symbolize their propensity for the magic arts.
1) The only two items in the entire Zelda series that can be argued to invoke the eye as a symbol for perception are the Lens of Truth and the Mask of Truth. But note that both items were created by the Sheikah and both items actually feature the Sheikah symbol (the handle of the Lens of Truth is shaped to form the tear), not the general eye symbol. In addition to this, it is said that the Lens/Mask of Truth were actually designed to expose the illusions created by Darkness, and so their actual symbolic nature is tied much more strongly to the Sheikah's "fighting evil" dogma than to a general "perception" symbol.
2) The appearance of the eye in correspondence to "mage enemies" is, as far as I'm aware, limited just to Agahnim. And even if it does appear with general mage enemies, it should be noted that the eye never appears in correspondence with benevolent magic, just evil magic.
3) I would also like to, once again, highlight that the most common object to be struck in order to defeat evil is the eye. Regardless of whether they are switches or enemy weakpoints, the eye is symbollically an obstacle in the path of justice.
While I don't doubt what you say about the symbolism of the eye in real-world culture, I don't think the Zelda mythology shares that same symbolism. All evidence leads us to deduce the eye is a symbol for evil.
It should, though. Relatable imagery and symbolism from a fictional work to real life can serve to make a fictional work more satisfying. I find the symbol of the eye to be a very old one and pops up in other cultures with similar implications, so I don't see why the eye shouldn't have similar connotations in a different but still somewhat similar culture as the culture of Hyrule.
In the Sheikah item's case, it can serve as a symbol for several ideas. The original Sheikah eye was a symbol for the misery that the Shiekah have faced and how they will always watch over the Royal Family. Also, the Sheikah also seem to have knowledge of some secret arts (used in the creation of magical items or maybe even fighting. I don't believe any other race has knowledge of these skills), so the eye is a viable symbol to embody these aspects of their race. The exposure of illusions is an aspect of increased perception as symbolized by an open eye. The Shiekah seem to be the lone example of the eye as a benevolent symbol of perception and knowledge of the hidden, however. Twili items also feature the eye, which fits due to the tribe's adept magic skills. The fused shadows hold malevolent power, but imp Midna's accessories also feature the eye and she is not wholly malevolent.
You also forgot Vaati, he has an eye motif going on. (-3-) Seems to be designed around it, even. Having a single eye as as weak point is also a common trope in videogames. Mythological creatures such as the Cyclops also had one eye. It can be used to make a creature seem more strange and alien while still providing a viable weakpoint rather than a symbol of their innate "evilness".