Bookmarks yes. Highlighting, don't think so. Haven't heard about it if it does. It's one of the weak links as far as using for educational purposes. Maybe it will be a late addition.
Nobody knows until we get the iPad in our hands. There'll be a lot of things that Apple did not list on their site or keynote that we'll find out on April 3rd. It is totally possible that the highlighting is there, just that Apple did not mention it.
In a way, that's good in a way that we'll still be more surprised with minor features.
Unlike the rest of the apple applications, I think iBook will evolute over times to include more features that people'll ask. It's going to be a money maker for Apple, so they have to spend some time on it.
Unlike Kindles and other e-ink readers, iPad is much more flexible in terms of adding more features and changing the whole layout as well.
I find annotating and highlighting on an actual kindle to be too much of a hassle - I would hope they would implement that functionality here as it stands to really benefit from a touch UI.