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.