S.S.
It's so scary when your baby has surgery, I know! But everything will be fine!! My oldest had surgery when he was 13 months old...I don't really want to get into what was done, but they had to rearrange skin. It was pretty involved. He also had tubes in his ears when he was 18 months old...which isn't a big deal, but I bawled when they put him under. He is perfectly fine! They're real troopers when they're little.
My friend's baby had to have surgery for pyloric stenosis (he was constantly throwing up and was always in pain) when he was like 2 months old. It's so scary, especially the younger they are, but he is perfectly fine too.
The doctors are skilled and will do everything they can for your daughter!! She'll be just fine! As for what to tell your son, if he's only 3, the simpler the better I think. Maybe say she has an owie on her eye and the doctors are going to fix it. If he has more questions, go from there.
Good luck!!