First of all, don't do the overnight. Golden Rule of Travel With Kids; get there as quickly as possible! You'll start waking up just as you arrive at the hotel and she'll be bouncing off the walls, after sleeping on the plane, and you'll be staring at the ceiling, really regretting doing this...
I think I've flown with my kids at every hour of the day. I have three and they were fine waking up early in the morning. They actually did worse leaving late at night. They just become groggy zombies when woken up in the wee hours, cooperative groggy zombies but they held it up until they could crash on the next flight.
Parents over-estimate their children's schedules. Kids lose their comfortable routines quickly when they're in a new situation. They also pick up on others' cues well. If everyone on the flight is sleeping, that helps them settle down. If they're in a busy airport with light, noise and lots of people, even if it's the middle of the night "their" time, they'll be alert and active.
When you travel, you're kind of in a Zone of No Time Universe. You sleep and eat when you can and wake up if you have to.