Does naked eye miss a lot between local stars and distant milkiness? When I look at the night sky I seem to resolve points which are local stars and milkiness at further regions of the galaxy. But what is between? I think there must be a lot of stars which are too faint to see individually, and yet not perceivable as part of a dense region of stars. Is this at all accurate? Does anybody know how much we fail to see when we think we are looking?
Even the Hubble telescope cannot "see" many of the stars and galaxies in the dark parts of space at first glance.  If they fix the Hubble on a dark patch for several days, the photons from extremely distant stars and galaxies will fill the image.

http://en.wikipedia.org/wiki/Hubble_Deep_Field

Also, the Earth's atmosphere will obscure and distort many stars that are visible from low Earth orbit and beyond.  Astronauts can see many more stars than we can.

Regarding your question, "how many are we missing", that's a tough one to answer. It depends on what level of detail you are talking about.