I love this idea.
You kind of see it in glass block windows with vents inset, but totally decoupling the functions could really free things up.
Screened openings with a fixed awning could have insulated doors on the inside, maybe coupled with
solar chimneys and earth tubes.
Clerestory windows go above head height, and offer great natural light.
The first room I had to myself had windows at head height to near the ceiling and they were perfect to me.
Cupolas are historically used for light and ventilation.
They do penetrate the roof deck, but are easier to make water impervious than sky
lights.
A vented cupola with a wind scoop inside could catch a lot of air, more if we could make it spin to face the breeze.
A windowed cupola already admits light from any compass direction, but inside the house, mirrors could be used to put it where you want it.
If you surround the cupola with a reflective roof, and give it a reflective ceiling, more light could be captured.
For windows that need not offer a view, what about using materials that are translucent but not transparent?
Some foam insulation fits this description.
What is the light transmission of an inch of styrofoam?
Glass or silicone filled with air bubbles might work.
Bubble wrap already exists, how about an inch thickness of it between two plates of glass?