Just how waterproof does it need to be? If it's to avoid drops and minor spillage wouldn't a ziplock freezer bag (well sealed and water-tested) work? I can understand though that if it is because it could be submerged that that wouldn't be enough though...
Scratch those ideas... Just tried with my Sony and the stylus only works about 1 time out of 5 when the screen is covered with a freezer bag.... I could still use it that way once the book is open because it has page turn buttons but the Kobo doesn't.
My tablets (Kobo Vox and Galaxy Tab), on the other hand work great in the bag with either a stylus or my finger...