Why is it studentem and not studenką?
Because it's your son and not your daughter. "Studentka" is a female student.
Is "student" only on college or generaly pupil?
In Polish it is very clear: you are an "uczeń/uczennica" until you start university education and become "student/studentka".
I assumed something like that. It is very similar to serbian.
Why is it a student". And is "student" rejected?
In my country we say someone is student when belonging to the group of students. This as answer on the question :Is your son working?
Well, I believe that it doesn't work in English without an article.
Why is it used in instrumental case instead of accusative?
You always use Instrumental in such sentences (X is Y), when Y is a noun phrase.
More info here: https://www.duolingo.com/comment/16373167
Thank you soooo much! That article was super useful :D