Why aren't backpacks waterproof? Because it's too expensive to do so.
If you consider how many seams there are in a backpack, and then trying to water proof all of those? Also, for the most part you don't need them to be. Sure you want your sleeping bag to be in a waterproof container most of the time, but actually all you do is make a condensation trap, what keeps moisture out, also keeps moisture in. And that applies to any fluid... including food aromas... body odours...
Even putting your sleeping bag in a dry bag too soon after vacating it, you risk trapping all that sweat you created during the night. Makes your bag stink.
If you look at photos of some of the big hikers, like Chris Townsend and the like, you'll notice when ever they stop for a cuppa, or lunch, they pull their sleeping bag out of the water proof stuff sack to air it.
So yes, a waterproof backpack sounds like a great idea, right up to the point when it isn't...
J