Does the pre-programme assignment of NIET have any marks? Does it matter? Are they checked?

It's difficult to say whether it matters or not because it is totally up to the college administration. When your first-year classes begin, they will ask you for the assignment and require you to submit it before the deadline.

However, there are some students who never submit any pre-programmed assignment. So, one thing is clear, that it does not have any grades, and it is only for practice and making students ready for their upcoming exams.