Mawa says that you need one atom to store one bit. With the buildup towards quantum computers and the recent breakthroughs with making the speed of light drop to zero with a gate laser, computers will be able to store information using sub-atomic particles and light.

As for the bigger question, Science Fiction will not be bothered with nanotechnology. Geosynchronous satellites were proposed by Arthur C. Clarke, but Science Fiction was not harmed when they were deployed. Once an item becomes reality, SciFi authors will come up with yet more far-fetched ideas. By the time we have a world with nanotechnology as common as a toaster, we'll be working on new ideas based off of the new sciences. Remember, the computer you're reading this with was a fantasy back in the 1960's, when spacecraft had the new cutting-edge 4K computers. Your digital watch has more computational power than the computers of the late 1950's. In the next ten years, everyone will have a Dick Tracy wrist video-telephone.

Perhaps the better question would be:

What will the dreamers and thinkers come up with when nanotechnology is commonplace?