Couldn't this be öffnen or öffnet?
I'm not sure what you mean. Did you get a fill-in-the-blank exercise for Sie ...... die Bücher where you had to choose from options including öffnen and öffnet? I can't find any such exercise. And such an exercise would indeed be ambiguous between sie öffnen "they open" and sie öffnet "she opens", so it would not be a good exercise.
If you had a listening exercise, you will have to write what the voice says, i.e. sie öffnen. If you had a translation exercise, you will have to translate what is written, i.e. sie öffnen to "they open". There is no choice of using öffnet.
What prompted your question? What kind of exercise did you have?