There should be small pieces of whatever they hit embedded in the body & glass of the aircraft. As long as they are analyzed, the cause of this won't remain a mystery forever.
My first thought was that this is more likely to be a spontaneous failure of the windshield glass under pressure, due to manufacturing flaw or improper maintenance. Things like that have certainly happened before. But then again, it seems weird that glass fragments would be projected inward in that scenario.
Plugging in 35k ft altitude, and 775 ft/s velocity here (https://www.spaceworks.aero/fcc2/index.html) gives dynamic pressure of 220 lb/ft2, vs ~2100 lb/ft2 for 1atm at sea level (the same calculator says 7k ft altitude has a static pressure of ~1600 lb/ft2, or rough idea of cabin air pressure).
At that height if windows are damaged enough to hurt captain or pilot, would the flight lose balance because of air coming in? How did they land in that situation? There is no mention of that in the article.
The laminated glass did not fully break. It appears only the inner layer shattered, and cabin pressure was not lost.
It has happened before that cockpit windows have failed at altitude resulting in explosive decompression, and the plane still landed successfully. For example, British Airways Flight 5390:
The airplane shouldn't be affected much by a blown out window. However, the blast in the captain's face might make it very difficult for him to see or even breath. If he could get his oxygen mask on, which I think has goggles, he should be ok.
