In my opinion you automatically anthropomorphise the ant as soon as you call it "she". It does, to my ear, endear the reader to the ant to a certain degree. After all, an owner who is particularly close to their dog will often refer to the hound as "he" or "she" rather than the onlooker's "it".
That said, that is maybe the desired effect.
An encyclopedia reference will likely use "it", since this is a creature we're talking about. I scanned the Wikipedia entry for "ant" and found only one reference to "she" and several to "it".
Hardly conclusive either. After all, David Attenborough regularly anthropomorphizes creatures as he observes them living their lives and endearing them to the viewer.
In short, it wouldn't sound out of place to me (the layperson) to use "she", but some thought must be given to the nature and purpose (scientific, entertainment etc) of the text or work in which the gender pronoun is used.