Yeah, I'm firmly in the "it actually happened" camp. All the stuff that "proves" otherwise is just tiny little bits of fluff that the internet took and ran with. Just look at what the internet did to bacon or kittens.I could see it as being a metaphorical way to tell the story of how he got over and accepted Navi's departure. That doesn't mean though that MM was a dream or whatever. But yeah I agree.
But yeah, I can't help but feel this really is MattPatt's fault. He's normally pretty good, but when it comes to Zelda his theories have been utter garbage. Except of course for his recent one about the hookshot, but that's because it's all physics and no philosophy. There really is absolutely no hard evidence to support that Link is dead. And the Elegy of Emptiness 'proof'? Let's examine things further.
First, the game text says the following about the Elegy:
"It's a mystical song that allows you to shed a shell shaped in your current image. By playing the song while wearing masks to assume different forms, you'll be able to leave up to four empty shells--one for each form!"
Notice it says nothing about souls or dead people or anything, just physical form.