It's ok to get water on her and in her if you make sure she dries thoroughly afterwards to avoid rusting in the future. All my ponies come second hand and they usually have their neck seal broken, so to make sure she dries thoroughly, I pop her head off and put her on a paper towel near a window for a few days to dry. Besides the eyes, you can wash her normally
For rusty eyes I just use toothpaste, a toothbrush, and a toothpick. Using the toothbrush, I scrub the majority of her eyes with toothpaste, then get the harder parts with a toothpick, minding her eyelashes. Then I rinse off the toothpaste. Some people use rust remover, but I never have, so I'm not sure about how to use it