I believe Merry did have a son. I also noticed he wasn't in the treeline, and was wondering why but these are good explanations. I don't think it was a typo; Tolkien wouldn't allow such a thing.
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Besides, poor Merry never did recieve much overt attention from the professor.
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As I read the Appendices, it seemed to me that Tolkien all but forgot Merry completely. Besides the omission of Merry's children in the family trees, did you notice that Merry's marrage to Estella isn't listed in the timeline? It has when Sam was married and when Pippin was married, but not Merry. Quite sad.
All too frustrating too, as I'm also writing a fic that centers around Merry during and post RotK. I've been working on it for... a while now. I hope to finish it this summer. It's a pretty depressing story line though... But hopefully it will be good when it's put together. I've spent hours hunched over my LotR books, painstakingly trying to make it as true to the books as possible. Man, that's hard. But it's worth it.