I think it's a nice theory, especially if you want to explain everything in-game. But I always have considered them part of the gameplay, in order to make the game work.
For example, in some games, such as Final Fantasy games, you gain experience and level up, which gives you abilities or more health so you can take more hits. In Zelda, I think that heart pieces/containers are a way to show an increase in Link's strength, stamina, and health.
So, I think they just fit in the game in a relatively un-explained way, just like finding rupees and hearts in the grass, being able to smash pots/enter people's houses, or having people tell you to press the action button to talk to them.
In terms of the paradox in the windmill ... I've been writing
OoT fanfiction for a while, and that was one thing I just sort of left alone. I don't think I'll ever be able to write a plausible explanation for that one.