Spaying/neutering will help the litter training process. But sometimes it can be a process and sometimes it does take some litter training before they get the hang of it. With my buns, we used a small area with a few litter boxes around. As they got better about using them, we would make the area bigger. They usually catch on pretty quickly and will continue to only go in the litter box. Every time they have an accident, wipe it up with a paper towel and throw it in their box. As they become better, you will be able to limit the number of litter boxes. But if they’re not spayed/neutered they may not catch on right away. Mine all did much better after their spay/neuters but it did take some time and effort with my Tans. I also did some clicker training with one of my buns who would just NOT use the litter box and it worked like a charm. After a week, his litter box habits improved greatly because of all the positive re-inforcement he was getting.
NEVER HIT YOUR RABBIT. It’s not only cruel because they don’t understand but also just does nothing but ruins your relationship with your rabbit. Your right, she probably does dislike you more for it so I’m confused why you would continue doing it if you knew it was causing that effect?