I imagine they do, but minimal, right? I have about 200 of them, and could probably delete z100 of them, but I bet deleting 100 might net me 50 mb of space.... I have reached a point where I don't want to delete anything from my iPad and have less than half a gig left.
I'd be surprised if all your bookmarks took up more than a few mb's at the very most, I really don't think you will see any space saving at all.