Yes, the file format is very different. There is forward-compatibility (FS9 terrain can be used in FSX), but FSX terrain cannot be used in FS9. FSX terrain is much more efficient, as it can contain multiple LODs in the same file, while FS9 terrain can only hold one LOD per file.
Theoretically, FSX and FS9 terrain made from the same source data should be nearly identical visually in the end result, though. FSX doesn't have an upper resolution limit, though when you get up past 10m, the visual range becomes so short that any advantages (except on the ground maybe) becomes dubious.
I might be skeptical about an LOD 13 Himalayan mesh, as I'm not aware of any 5m source data for the Himalayans (that doesn't mean it doesn't exist, just that I'm not aware of it), and just because it may be compiled at LOD 13, if it isn't made with 5m source data there is no advantage or extra detail, just huge files. And LOD13 terrain mesh wouldn't be visual more than a few kilometers from your aircraft, so from altitude you won't see much difference, and would see no difference from a distance.