Although Bernadette doesn't perform her disappearing act until the back half of the novel, it's obvious what's going to happen as soon as you read the title Where'd You Go, Bernadette?. We see the question as being spoken from Bee's perspective, as she's the "author" of the book.
The title is also as an allusion to Bernadette's fall from grace. In this light, the title isn't about where Bernadette is in the Carmen Sandiego sense, but rather in terms of her relationship with her past...how she moved from "Bernadette Past" to "Bernadette Present" (1.741). We spend just as much time uncovering this transition as we do scouring the planet for our Houdini wannabe.