Native English speaker here. In my opinion, saying "She only eats fruit" makes sense because it doesn't specify what kind of fruit per se. But conversely "She only eats vegetables" makes sense but "She only eats vegetable" doesn't flow right. Anyways there is no hard or fast rules in English since like all languages, it is a dynamic form since it is susceptible to change.
Basically, you'd be using the word "fruit" as a category rather than a countable noun if you say "she only eats fruit". That's why it's a natural thing to say. Although it's equally fine to say "she only eats fruits", but then it's a countable noun. Not really any difference in meaning just two ways of putting it.