Hi Victoria!
Our princesses, they are something aren't they?
I've taken my daughter to Bibbidi Bobbidi Boutique a few times, including when she was 3.
For the price, I'd say get your money's worth. When my daughter was 3, she got her makeover first thing in the morning (she got, of course, the Princess hairstyle). She also wore her favorite Princess costume. Once the makeover was done, my daughter wanted to remain that way the entire day. She loved the extra attention she got, and she was very happy. I'd say go for the morning so she has the whole day to look and be treated like a princess. We took her to the Boutique that morning at Cinderella's Castle, then walked her over to Cinderella's Royal Table for Breakfast. That made her day!
I'd say we got her hair done that year somewhere near the end of the vacation. If you're concerned, I would shoot for a reservation somewhere in the middle or end of the vacation. And you're right, my daughter wanted to keep that hairstyle to the point where it was no longer the perfect bun :-)
May you, princess, and family have a wonderful time!