They are somewhat smaller, but this alone doesn't have to be such a big issue. I and others have made good looking henchmen out of grots so too small is not really such a big issue with henchmen. They where just mutants or children.
The real issue is that
Lotr miniatures are realistically proportioned and
40k models are not. This makes them look strange (with their silly small heads, and flimsy weapons etc.) and unusable without some conversions.