Yeah I totally agree.
And the whole issue of guardian existence gets really tricky, especially when you try to make theories work with both ‘dead’ guardians and with Shin. Sometimes you just have to throw your hands up and yell “Space Magic!”
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And Light is also paracausal. Guardians decide their own fate
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The explanation that most Guardians are dead is what really puts the matter to bed for me. Though it’s plausible that the Traveler could protect us as well.
Shin’s Light is extremely powerful; even latent both Jaren and his Ghost, as well as Dredgen Yor, could sense his potential. He’s also the first Hunter to use Golden Gun on record. It’s pretty reasonable to assume he developed the technique himself, since he’s already been to the Tower and around other Guardians, yet the sequence isn’t written in a way that suggests he’s ever seen or experienced anything like it. It happens on instinct. And, of course, the weapon avatar in Golden Gun is The Last Word.
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Oryx cannot Take paracausal beings. He also can only take biological things. This is why he can Take Vex-their mind fluid is biological-but he cannot Take shanks/servitors/etc.
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I’d say there’s an exception to the “cannot Take paracausal beings”, though. If they fail to stand up to him, then by the logic of the sword, if he defeats them, he can Take them.
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I guess we’ll never find out for sure.
Until Mr. Dickinson writes more high-quality tier work like the Books again. 
Wait, how do we know that “Shin Malphur” isn’t just the name he gave himself after being resurrected?
The real hole in the theory in my opinion is Ana Bray because there’s no way she would give herself the surname “Bray” without reason right?
WAIT, I just remembered. 
Shin Malphur got his ghost while being a survivor of the collapse. So he never died.
It’s really weird that he just picked it up when Dredgen Yor killed Jaren Ward.
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I don’t think Shin just picked up the Ghost. He found it hovering over Jaren’s body and it encouraged him to take up The Last Word, and accompanied him from there on.
It, Jaren, Dredgen Yor, and Dredgen Yor’s Ghost sensed something different about Shin, perhaps that the Traveler’s light was latent inside him, and that’s ostensibly what led Yor to leave him the weapon and the Ghost to bond to him.
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But isn’t it strange that the ghost chose a live host?
Maybe it chose him because he was already ready to become a Guardian and didn’t need to die? There are always exceptions to every rule (although bear in mind I’m new to the Lore so I’m now off to read up on it).
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There’s always exceptions, yes. And don’t worry, you’ll catch up. 
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Why didn’t he take Dregs, Legionaries and Collosi? They are biological beings…
To bring up another interesting point about Oryx taking Vex:
Since the Vex’s mind-fluid is biological, he is able to take Vex without an issue. So when Vex are taken, what happens to the mind-fluid itself? Is it corrupted by the power of the Darkness/Deep and cut away from the rest of the Vex network? The Vex mind-fluid connects every piece of Vex technology, including the unstable centaur, Nessus and The Black Garden on Mars. So if Oryx went and took all of the Vex that he did, surely the mind-fluid would have told the rest of the Vex “Hey wait something’s not right here tf”… You know?
If Oryx knew the full extent of the Vex mind-fluid, he could have, in theory, controlled the entirety of the Vex network by simply taking a few Vex and corrupting the fluid inside.
So big question: How exactly does Vex mind-fluid work?
More in-depth and on-topic question: What happened to the mind-fluid inside Taken Vex?
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Apparently. That’s what happened to the Seditious Mind:
The great fortress of your thoughts has been breached, your unity broken. The network around and within you lies ruptured. You are cut out from the fabric, a hole in the whole.
This is the first choice you have ever been given.
So, the Taken Vex aren’t exactly ‘Vex,’ i.e., they’re no longer part of the Vex network. Taken Vex, in this case the Seditious Mind, go from part of the hivemind to an individual.
The Vex presumably did know about the Taken threat. The possibility of the Taken ‘infecting’ the Vex collective mind was why Paradox was such a crucial mission back in TTK. As Ikora says:
Ikora: If the Taken are here in the vault, they are at the heart of the Vex collective mind. Imagine the machine-planets of the Vex surging with Taken power. This must not be, Guardian.
This blight is probably why the Vex let Praedyth send out a message in the first place, in order to rid the Vault of the Taken:
Praedyth: [static] a message. The creatures will soon reach the heart of the vault. When [static] once they take the Vex, they’ll come for the Light.
Praedyth: [static] I don’t know why they’re letting me speak. Now, after so long.
Praedyth: Enslaved to a will they don’t understand. A will long dead here. Dead eons ago. But then, they won’t end, will they? Because you’re here.
Given that the act of Taking separates the Vex from the Collective, it’s probably not as simple as taking just a few Vex and letting the blight spread through the Network. That’s why the Taken had to (attempt to) infect the Vault, because it’s such a vital part of the collective mind. It’s entering spinfoil territory, but that may be why Quria didn’t introduce the Worms into its mind fluid- because it would spread to the whole of the network, as opposed to simply being Taken, which separates units from the network.
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That’s an extremely solid post and I agree with you.
The Vex would logically quarantine any viruses in the sytem because why would they keep them in?
I think what he means is that our ghost is keeping a copy of our mind inside it, and from the moment it resurrects us it constantly “refreshes it” (so to speak) so that it’s in sync with our current mind, so when we are killed and it resurrects us it is inserting this copy of our mind into the body.
The nail has been hit on the head with this I think