did red kill dr nik for assisting with the cover up
I am unclear if red killed or just questioned dr nik
They never really showed what happened to Dr. Nik, and we haven't seen him since. But the writer of that episode answered that exact question on twitter shortly after it aired. He said that when Red left the room, that Dr. Nik was alive.
(If I remember correctly the writer was Daniel Knauf and the questioning took place in "Cape May.")
But... that doesn't rule out the possibility that someone else killed Dr. Nik later, after Red left. So I guess his fate is unknown. Maybe Red isn't done with his... revenge.