Wow, that is a complicated situation, and let me congratulate you for being so understanding, thoughtful, and sensitive towards your babysitter. It can't be easy hearing those things, especially when the welfare of your children was involved. You had no way to know she was bipolar. While it is true there are signs, many of us are very good at disguising them, and have a great deal of control when we need to, with exceptions of course. I can only speak for myself, but yes, if I am manic and children are being very loud (being children!!) it really grates on my nerves. I have never hurt a child, but I suppose the risk is always there. It might be interesting to see what some of the moms here have to say (I still have no kids!)
As far as asking her if she hurt them...that's a tough one. If she says no, will you believe it? Will it help? If she says yes, will that help? How will you respond? These are all things you can ask yourself.
She is right, there are good days and bad. It is very reasonable to assume that she has been well, up until the point she told you she wasn't. Especially considering she came to you when she needed help and has been very willing to be honest and share her feelings, some that included the welfare of your children. If she was hurting htem, I tend to think that she would not be so honest and forthright, but of couorse, I could be wrong. What does your gut tell you? When was she diagnosed? Has she been taking her meds? Are they working?
In the end, it is hard to know why your little one is fussing like that at night...it could be many things. A visit to the pediatrician might be in order to discuss behaviour, or maybe even someone here can share their stories about children around your little ones age. It could be totally unrelated. Did you ever see any physical signs of abuse (ie unusual bruises-not the ones little ones get from falling or bumping into things)
I am sorry I could not be more definitive. Again, thank you for not perpetrating stigmas, and coming to the source to help you in your journey here. This could not have been easy...