The reason the hobbits have never met Bombadil is because they only venture into the very fringes of the Old Forest. Likewise, the fact that his home is less than twenty miles from the road to the Grey Havens is irrelevant; if you've ever walked a long distance on foot, you know that twenty miles is nothing to sneeze at in a straight line. Draw a circle with a twenty mile radius from the road and you have over 1200 square miles of territory; it's not surprising that the elves wouldn't have run across him, especially since he doesn't like to be found. This is all splitting hairs though, because it's clear that some elves know of him. They don't know much about him, but they do have a name for him.
The idea that he's lying about how he knew the hobbits were coming is not supported by the story. Tom is at one with the forest; he certainly could have heard the rumor of their passing from the trees. Likewise, it's not hard to imagine that Tom does talk to Farmer Maggott from time to time. Maggott is taciturn and grim; not the type to go tell stories around the Shire about his weird mystical friend in the Old Forest. Also, hobbits are plain, practical folk, likely to dismiss such outlandish tales (see their reactions in the early part of Fellowship to stories of giants).
I really don't see why you think the Old Forest is the second-most dangerous place in Middle-Earth. It's probably not even the tenth most dangerous of the small subset of places that Tolkien actually described. It's an uncanny, unwelcoming place, sure. Is it more dangerous than the Paths of the Dead, which only one living man may walk and survive? Is it more dangerous than Barad-Dur, home of Sauron, or Cirith Ungol, home of the deadliest of Ungoliant's spawn? More dangerous than Mirkwood, where stepping off the paths without the protection of Thranduil's wood-elves is nearly a death sentence? More dangerous than Dagorlad, where will-o-wisps lead travellers astray to drown in the ghost-haunted swamps? Furthermore, the Barrow-Downs may be in some sense part of Tom's "country", but as he and Goldberry make clear, Tom does not control his country. Rather, he is an integrated part of it. It would not be his style to purge the countryside of all evil simply because he could. He seems to be some sort of nature spirit, content to let be what already is, unless urgent need and his responsibilities as a host take precedence.
I think you really got confused when you said that all of the trees in the Old Forest are huorns. I don't think that's true at all; are you confusing the Old Forest with Fangorn? Even in Fangorn we don't have a clear indication that ALL of the trees are huorns. Old Man Willow seems to be a kind of huorn, or something related to them, but nowhere are we given an indication that the trees of the foreboding Old Forest are anything more than trees that resent the presence of intruders. Don't forget that Tolkien had a deep reverence for trees, and considered them living creatures that could feel pain, and that he could commune with.
You theorize that Bombadil was in Middle-Earth "before Morgoth set foot there." This is impossible because Morgoth (then known as Melkor) went to Arda as soon as it was created. You theorize that Bombadil was "ruler of the darkness" before Morgoth -- since Morgoth created the darkness by throwing down the Two Lamps, I don't see how that's possible.
I think a lot of the problem people have with Tom Bombadil is that he is deliberately presented as a mystery. He doesn't fit neatly into our categories of good and evil. It's fun to speculate about who or what he might be, but I don't think even Tolkien knew. And honestly, I think you've strayed very far from what he intended or what is supportable in the text with this guess.
