Not sure what you mean by 'run rampant'. OMW lures unwary travelers to their doom, but there aren't very many in
the Old Forest. As far as keeping OMW from eating people,
Tom can't be everywhere at once, and doesn't expect a lot of visitors in his domain.
The
Hobbits have never heard of him (assuming you mean Tom here) because they've never been to the OF before and they don't interact with Farmer Maggot that much.
As far as
Beorn, he is another enigma, though, unlike Tom, probably not intentional. Or perhaps 'disparity' is a better word.
The Hobbit was not originally meant to be part of the legendarium, therefore
Tolkien was not held by the rules he established in said mythology. When Tolkien made TH part of the legendarium, he didn't change Beorn in
The Hobbit, but when Beorn and his kin are mentioned in
The Lord of the Rings, their skin-changing is not; it's sort of swept under the rug, because human
skin-changers are not a thing in the legendarium.
Mermaid? Where on earth do you get that idea? 🤨 She's a spirit of the River Withy-windle. Do we really need to know more than that? If you don't see rhyme or reason in them, again, that's intentional on Tolkien's part.
They don't really need to. And I find amusing your attempts to make sense of Tom and GB, when you're willing to overlook anomalies in the films. It's fine when they don't make sense, I guess 😄
Baffling, maybe. Nonentity? Nah, I disagree.
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None of these apply to
Tom Bombadil.